[gmx-users] total charge of the system

[ahmet yıldırım]

Hi,

In my simulation, total charge of the system is a noninteger number (System
has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine
atoms.
Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

Fatal error:
moleculetype CU1 is redefined
is it some thing wrong?

Below is the first and final version of the .top file:

First topol.top File
**
[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L  1
Protein_chain_H 1
SOL 10
SOL127
SOL157
SOL 41779
**

Final topol.top File
*#include "ions.itp"*

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L  1
Protein_chain_H 1
SOL 10
SOL127
SOL157
SOL *41771*
*CL- 8*






-- 
Ahmet YILDIRIM
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Re: [gmx-users] total charge of the system

[Mark Abraham]

On 01/25/11, ahmet yıldırım   wrote:
> Hi,
> 
> In my simulation, total charge of the system is a noninteger number (System 
> has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine 
> atoms. 
> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> 
> 
> Fatal error:
> 
> moleculetype CU1 is redefined
> is it some thing wrong?
> 

ions.itp defines molecule types for ions. Molecule types cannot be redefined. 
When you #included ions.itp GROMACS thought you were doing illegal 
redefinitions. Look back in the .top to find the original definitions, and then 
take suitable action.

Mark


> 
> 
> Below is the first and final version of the .top file:
> 
> 
> First topol.top File
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L  1
> Protein_chain_H 1
> SOL 10
> SOL    127
> 
> SOL        157
> SOL 41779
> 
> 
> Final topol.top File
> #include "ions.itp"
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L  1
> 
> Protein_chain_H 1
> SOL 10
> SOL    127
> SOL        157
> SOL 41771
> CL-         8
> 
> 
> 
> 
> 
> 
> 
> -- 
> Ahmet YILDIRIM
> 
> 
>
-- 
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Re: [gmx-users] total charge of the system

[ahmet yıldırım]

Dear Mark,

I looked at gromacs mail list but I could not find a proper solution
.Whatshould
I add to the .top file? Please look at the following reconstructed1 .top and
reconstructed1 .top files

I have error as the following reconstructed1 .top file:
*Fatal error:*
moleculetype CU1 is redefined

I have error as the following reconstructed2 .top file:
*Fatal error:*
No such moleculetype CL-
*
Original .top file:*
; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41779

*reconstructed1 .top file*
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
*#include "ions.itp"*

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 4177*1*
CL-   *8*
*reconstructed2 .top file*
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
**
[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 4177*1*
CL-   *8*


25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:

>
>
> On 01/25/11, *ahmet yıldırım *  wrote:
>
> Hi,
>
> In my simulation, total charge of the system is a noninteger number (System
> has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine
> atoms.
> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
> Fatal error:
> moleculetype CU1 is redefined
> is it some thing wrong?
>
>
> ions.itp defines molecule types for ions. Molecule types cannot be
> redefined. When you #included ions.itp GROMACS thought you were doing
> illegal redefinitions. Look back in the .top to find the original
> definitions, and then take suitable action.
>
> Mark
>
>
>
>
> Below is the first and final version of the .top file:
>
> First topol.top File
> **
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L  1
> Protein_chain_H 1
> SOL 10
> SOL127
> SOL157
> SOL 41779
> **
>
> Final topol.top File
> *#include "ions.itp"*
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L  1
> Protein_chain_H 1
> SOL 10
> SOL127
> SOL157
> SOL *41771*
> *CL- 8*
>
>
>
>
>
>
> --
> Ahmet YILDIRIM
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] total charge of the system

[Mark Abraham]

On 01/25/11, ahmet yıldırım   wrote:
> Dear Mark,
> 
> I looked at gromacs mail list but I could not find a proper solution .What 
> should I add to the .top file? Please look at the following reconstructed1 
> .top and reconstructed1 .top files
> 
> 
> I have error as the following reconstructed1 .top file:
> 
> Fatal error:
> 
> moleculetype CU1 is redefined
> 
> 
> I have error as the following reconstructed2 .top file:
> 
> Fatal error:
> 
> No such moleculetype CL-
> 
> 

I don't have any knowledge of the context, so can't answer. It looks to me like 
you are mixing copies of ions.itp from multiple sources. Don't. Use the one for 
the force field you are targetting. pdb2gmx generated the right invocation - 
all you should have to do is use that by generating correctly-named ions. See 
http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion)

Mark


> Original .top file:
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 
> ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL    10
> SOL   127
> SOL   157
> SOL 41779
> 
> 
> reconstructed1 .top file
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> #include "ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 
> ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL    10
> SOL   127
> SOL   157
> SOL 41771
> 
> CL-           8
> reconstructed2 .top file
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 
> ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL    10
> SOL   127
> SOL   157
> SOL 41771
> 
> CL-           8
> 
> 
> 25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:
> 
> > 
> > 
> > 
> > On 01/25/11, ahmet yıldırım   wrote:
> > > 
> > > Hi,
> > > 
> > > In my simulation, total charge of the system is a noninteger number 
> > > (System has non-zero total charge: 8.04e+00). I neutralized it with 8 
> > > chlorine atoms. 
> > > Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> > > 
> > > 
> > > 
> > > Fatal error:
> > > 
> > > moleculetype CU1 is redefined
> > > is it some thing wrong?
> > > 
> > 
> > 
> > ions.itp defines molecule types for ions. Molecule types cannot be 
> > redefined. When you #included ions.itp GROMACS thought you were doing 
> > illegal redefinitions. Look back in the .top to find the original 
> > definitions, and then take suitable action.
> > 
> > 
> > Mark
> > 
> > 
> > 
> > > 
> > > 
> > > Below is the first and final version of the .top file:
> > > 
> > > 
> > > 
> > > First topol.top File
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L  1
> > > Protein_chain_H 1
> > > SOL 10
> > > SOL    127
> > > 
> > > 
> > > SOL        157
> > > SOL 41779
> > > 
> > > 
> > > Final topol.top File
> > > #include "ions.itp"
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L  1
> > > 
> > > 
> > > Protein_chain_H 1
> > > SOL 10
> > > SOL    127
> > > SOL        157
> > > SOL 41771
> > > CL-         8
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > -- 
> > > Ahmet YILDIRIM
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > 
> > --
> > 
> > gmx-users mailing list    gmx-users@gromacs.org
> > 
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > 
> > Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > 
> > Please don't post (un)subscribe requests to the list. Use the
> > 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > 
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > 
> 
> 
> 
> 
> -- 
> Ahmet YILDIRIM
> 
> 
>
-- 
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[gmx-users] Re: Secondary structure loss in implicit solvent simulations

[K. Singhal]

Hi

It's not necessarily GPU-specific, it's implicit solvent-specific. I don't get 
these problems in explicit solvent simulations on CPU, only in implicit solvent 
simulations both on GPU as well as CPU. One of the problems that I can think of 
is unbalanced charges that I would have balanced out using NaCl ions, but not 
any more.

Regards
Kush



--
Kushagra Singhal
Promovendus, Computational Chemistry
van 't Hoff Institute of Molecular Sciences
Science Park 904, room C2.119
1098 XH Amsterdam, The Netherlands
+31 205256965
Universiteit van Amsterdam
k.sing...@uva.nl


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Antw: Re: [gmx-users] total charge of the system

[Emanuel Peter]

Hello,

You have to look into your ions.itp which is included in your top-file by
#include ions.itp.
There all the types of ions have to be defined.
The atom-types which you can see in the ions.itp, you will
find in the ff"your-forcefield".itp where your atomtypes are defined.
On top of your .top file the Atomtype-itp-file is included.
All these files are normally placed in /usr/share/gromacs/top/.
But you also can place them into your current directory.

Bests,

Emanuel

>>> Mark Abraham  25.01.11 10.48 Uhr >>>


On 01/25/11, ahmet yıldırım   wrote:Dear Mark,

I looked at gromacs mail list but I could not find a proper solution .What
should I add to the .top file? Please look at the following reconstructed1 .top
and reconstructed1 .top files

I have error as the following reconstructed1 .top file:
Fatal error:
moleculetype CU1 is redefined

I have error as the following reconstructed2 .top file:
Fatal error:
No such moleculetype CL-


I don't have any knowledge of the context, so can't answer. It looks to me like
you are mixing copies of ions.itp from multiple sources. Don't. Use the one for
the force field you are targetting. pdb2gmx generated the right invocation -
all you should have to do is use that by generating correctly-named ions. See
http://www.gromacs.org/Documentation/Gromacs_Utilities/genion

Mark

Original .top file:
; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41779

reconstructed1 .top file
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
#include "ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41771
CL-   8
reconstructed2 .top file
; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41771
CL-   8


25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:


On 01/25/11, ahmet yıldırım   wrote:Hi,

In my simulation, total charge of the system is a noninteger number (System has
non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. 
Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

Fatal error:
moleculetype CU1 is redefined
is it some thing wrong?


ions.itp defines molecule types for ions. Molecule types cannot be redefined.
When you #included ions.itp GROMACS thought you were doing illegal
redefinitions. Look back in the .top to find the original definitions, and then
take suitable action.

Mark





Below is the first and final version of the .top file:

First topol.top File

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L  1
Protein_chain_H 1
SOL 10
SOL127
SOL157
SOL 41779


Final topol.top File
#include "ions.itp"

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L  1
Protein_chain_H 1
SOL 10
SOL127
SOL157
SOL 41771
CL- 8






-- 
Ahmet YILDIRIM




--
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-- 
Ahmet YILDIRIM


-- 
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Re: Re: [gmx-users] total charge of the system

[ahmet yıldırım]

Dear Mark and Emanuel,

I am sending the ions.tip and the topol.top files. Everything seems ok. Any
problem about these files?

By the way, I am using the Gromacs 4.5.3.
Force Field 43a1

25 Ocak 2011 12:03 tarihinde Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> yazdı:

> Hello,
>
> You have to look into your ions.itp which is included in your top-file by
> #include ions.itp.
> There all the types of ions have to be defined.
> The atom-types which you can see in the ions.itp, you will
> find in the ff"your-forcefield".itp where your atomtypes are defined.
> On top of your .top file the Atomtype-itp-file is included.
> All these files are normally placed in /usr/share/gromacs/top/.
> But you also can place them into your current directory.
>
> Bests,
>
> Emanuel
>
> >>> Mark Abraham 25.01.11 10.48 Uhr >>>
>
>
>
> On 01/25/11, *ahmet yıldırım *  wrote:
>
> Dear Mark,
>
> I looked at gromacs mail list but I could not find a proper solution 
> .Whatshould
> I add to the .top file? Please look at the following reconstructed1 .top
> and reconstructed1 .top files
>
> I have error as the following reconstructed1 .top file:
> *Fatal error:*
> moleculetype CU1 is redefined
>
> I have error as the following reconstructed2 .top file:
> *Fatal error:*
> No such moleculetype CL-
> **
>
>
> I don't have any knowledge of the context, so can't answer. It looks to me
> like you are mixing copies of ions.itp from multiple sources. Don't. Use the
> one for the force field you are targetting. pdb2gmx generated the right
> invocation - all you should have to do is use that by generating
> correctly-named ions. 
> Seehttp://www.gromacs.org/Documentation/Gromacs_Utilities/genion
>
> Mark
>
> *Original .top file:*
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
>
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
> ANTIBODY 2F5 HEAVY CHAIN in water
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL10
> SOL   127
> SOL   157
> SOL 41779
>
> *reconstructed1 .top file*
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> *#include "ions.itp"*
>
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
> ANTIBODY 2F5 HEAVY CHAIN in water
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL10
> SOL   127
> SOL   157
> SOL 4177*1*
> CL-   *8*
> *reconstructed2 .top file*
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> **
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
> ANTIBODY 2F5 HEAVY CHAIN in water
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL10
> SOL   127
> SOL   157
> SOL 4177*1*
> CL-   *8*
>
>
> 25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:
>
>>
>>
>> On 01/25/11, *ahmet yıldırım *  wrote:
>>
>> Hi,
>>
>> In my simulation, total charge of the system is a noninteger number
>> (System has non-zero total charge: 8.04e+00). I neutralized it with 8
>> chlorine atoms.
>> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>>
>> Fatal error:
>> moleculetype CU1 is redefined
>> is it some thing wrong?
>>
>>
>> ions.itp defines molecule types for ions. Molecule types cannot be
>> redefined. When you #included ions.itp GROMACS thought you were doing
>> illegal redefinitions. Look back in the .top to find the original
>> definitions, and then take suitable action.
>>
>> Mark
>>
>>
>>
>>
>>
>> Below is the first and final version of the .top file:
>>
>> First topol.top File
>> **
>> [ molecules ]
>> ; Compound#mols
>> Protein_chain_P 1
>> Protein_chain_L  1
>> Protein_chain_H 1
>> SOL 10
>> SOL127
>> SOL157
>> SOL 41779
>> **
>>
>> Final topol.top File
>> *#include "ions.itp"*
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein_chain_P 1
>> Protein_chain_L  1
>> Protein_chain_H 1
>> SOL 10
>> SOL127
>> SOL157
>> SOL *41771*
>> *CL- 8*
>>
>>
>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Ahmet YILDIRIM

Re: Re: [gmx-users] total charge of the system

[Mark Abraham]

On 01/25/11, ahmet yıldırım   wrote:
> Dear Mark and Emanuel,
> 
> I am sending the ions.tip and the topol.top files. Everything seems ok. Any 
> problem about these files?
> 

No. So one of the other #include files is erroneously defining ion molecule 
types. See www.gromacs.org/Documentation/Include_File_Mechanism. Go and read 
them and fix it.

As the link I sent last time hinted, you need to name *molecules* in the 
[molecules] directive. Look carefully at the *molecule* name of chloride where 
it is defined.

Mark

> 
> 
> 
> By the way, I am using the Gromacs 4.5.3.
> Force Field 43a1
> 
> 25 Ocak 2011 12:03 tarihinde Emanuel Peter 
>  yazdı:
> 
> 
> > Hello,
> > 
> > You have to look into your ions.itp which is included in your top-file by 
> > #include ions.itp.
> > 
> > There all the types of ions have to be defined.
> > The atom-types which you can see in the ions.itp, you will
> > find in the ff"your-forcefield".itp where your atomtypes are defined.
> > On top of your .top file the Atomtype-itp-file is included.
> > 
> > All these files are normally placed in /usr/share/gromacs/top/.
> > But you also can place them into your current directory.
> > 
> > Bests,
> > 
> > Emanuel
> > 
> > >>> Mark Abraham  25.01.11 10.48 Uhr >>>
> > 
> > 
> > 
> > 
> > 
> > On 01/25/11, ahmet yıldırım   wrote:
> > > 
> > > Dear Mark,
> > > 
> > > I looked at gromacs mail list but I could not find a proper solution 
> > > .What should I add to the .top file? Please look at the following 
> > > reconstructed1 .top and reconstructed1 .top files
> > > 
> > > 
> > > 
> > > I have error as the following reconstructed1 .top file:
> > > 
> > > Fatal error:
> > > 
> > > moleculetype CU1 is redefined
> > > 
> > > 
> > > I have error as the following reconstructed2 .top file:
> > > 
> > > Fatal error:
> > > 
> > > No such moleculetype CL-
> > > 
> > > 
> > 
> > I don't have any knowledge of the context, so can't answer. It looks to me 
> > like you are mixing copies of ions.itp from multiple sources. Don't. Use 
> > the one for the force field you are targetting. pdb2gmx generated the right 
> > invocation - all you should have to do is use that by generating 
> > correctly-named ions. See 
> > http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion)
> > 
> > 
> > Mark
> > 
> > 
> > > Original .top file:
> > > ; Include topology for ions
> > > #include "gromos43a1.ff/ions.itp"
> > > 
> > > 
> > > [ system ]
> > > ; Name
> > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; 
> > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> > > 
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L 1
> > > Protein_chain_H 1
> > > SOL    10
> > > SOL   127
> > > SOL   157
> > > SOL 41779
> > > 
> > > 
> > > 
> > > reconstructed1 .top file
> > > ; Include topology for ions
> > > #include "gromos43a1.ff/ions.itp"
> > > #include "ions.itp"
> > > 
> > > [ system ]
> > > ; Name
> > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; 
> > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> > > 
> > > 
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L 1
> > > Protein_chain_H 1
> > > SOL    10
> > > SOL   127
> > > SOL   157
> > > SOL 41771
> > > 
> > > 
> > > CL-           8
> > > reconstructed2 .top file
> > > ; Include topology for ions
> > > #include "gromos43a1.ff/ions.itp"
> > > 
> > > [ system ]
> > > ; Name
> > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; 
> > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> > > 
> > > 
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L 1
> > > Protein_chain_H 1
> > > SOL    10
> > > SOL   127
> > > SOL   157
> > > SOL 41771
> > > 
> > > 
> > > CL-           8
> > > 
> > > 
> > > 25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:
> > > 
> > > 
> > > > 
> > > > 
> > > > 
> > > > On 01/25/11, ahmet yıldırım   wrote:
> > > > > 
> > > > > 
> > > > > Hi,
> > > > > 
> > > > > In my simulation, total charge of the system is a noninteger number 
> > > > > (System has non-zero total charge: 8.04e+00). I neutralized it 
> > > > > with 8 chlorine atoms. 
> > > > > Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > Fatal error:
> > > > > 
> > > > > moleculetype CU1 is redefined
> > > > > is it some thing wrong?
> > > > > 
> > > > 
> > > > 
> > > > ions.itp defines molecule types for ions. Molecule types cannot be 
> > > > redefined. When you #included ions.itp GROMACS thought you were doing 
> > > > illegal redefinitions. Look back in the .top to find the original 
> > > > definitions, and then 

Re: Re: [gmx-users] total charge of the system

[ahmet yıldırım]

Dear Mark,

A million thanks. Problem is solved.
Finally,
Select a continuous group of solvent molecules:
...
Group12 (  Water) has 126219 elements
Group13 (SOL) has 126219 elements

Which one should I choose 12 or 13?

*Final topol.top file:


*;File 'topol.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Tue Jan 25 10:12:14 2011
;
;This is a standalone topology file
;
;It was generated using program:
;pdb2gmx - VERSION 4.5.3
;
;Command line was:
;pdb2gmx -f 3MOA.pdb -water spc -ter
;
;Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "gromos43a1.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_P.itp"
#include "topol_Protein_chain_L.itp"
#include "topol_Protein_chain_H.itp"

; Include water topology
#include "gromos43a1.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41771
*CL 8
*


25 Ocak 2011 13:13 tarihinde Mark Abraham  yazdı:

>
>
> On 01/25/11, *ahmet yıldırım *  wrote:
>
> Dear Mark and Emanuel,
>
> I am sending the ions.tip and the topol.top files. Everything seems ok. Any
> problem about these files?
>
>
> No. So one of the other #include files is erroneously defining ion molecule
> types. See www.gromacs.org/Documentation/Include_File_Mechanism. Go and
> read them and fix it.
>
> As the link I sent last time hinted, you need to name *molecules* in the
> [molecules] directive. Look carefully at the *molecule* name of chloride
> where it is defined.
>
> Mark
>
>
>
> By the way, I am using the Gromacs 4.5.3.
> Force Field 43a1
>
> 25 Ocak 2011 12:03 tarihinde Emanuel Peter <
> emanuel.pe...@chemie.uni-regensburg.de> yazdı:
>
>> Hello,
>>
>> You have to look into your ions.itp which is included in your top-file by
>> #include ions.itp.
>> There all the types of ions have to be defined.
>> The atom-types which you can see in the ions.itp, you will
>> find in the ff"your-forcefield".itp where your atomtypes are defined.
>> On top of your .top file the Atomtype-itp-file is included.
>> All these files are normally placed in /usr/share/gromacs/top/.
>> But you also can place them into your current directory.
>>
>> Bests,
>>
>> Emanuel
>>
>> >>> Mark Abraham 25.01.11 10.48 Uhr >>>
>>
>>
>>
>>
>> On 01/25/11, *ahmet yıldırım *  wrote:
>>
>> Dear Mark,
>>
>> I looked at gromacs mail list but I could not find a proper solution .
>> What should I add to the .top file? Please look at the following
>> reconstructed1 .top and reconstructed1 .top files
>>
>> I have error as the following reconstructed1 .top file:
>> *Fatal error:*
>> moleculetype CU1 is redefined
>>
>> I have error as the following reconstructed2 .top file:
>> *Fatal error:*
>> No such moleculetype CL-
>> **
>>
>>
>> I don't have any knowledge of the context, so can't answer. It looks to me
>> like you are mixing copies of ions.itp from multiple sources. Don't. Use the
>> one for the force field you are targetting. pdb2gmx generated the right
>> invocation - all you should have to do is use that by generating
>> correctly-named ions. 
>> Seehttp://www.gromacs.org/Documentation/Gromacs_Utilities/genion
>>
>> Mark
>>
>> *Original .top file:*
>> ; Include topology for ions
>> #include "gromos43a1.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
>> ANTIBODY 2F5 HEAVY CHAIN in water
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein_chain_P 1
>> Protein_chain_L 1
>> Protein_chain_H 1
>> SOL10
>> SOL   127
>> SOL   157
>> SOL 41779
>>
>> *reconstructed1 .top file*
>> ; Include topology for ions
>> #include "gromos43a1.ff/ions.itp"
>> *#include "ions.itp"*
>>
>> [ system ]
>> ; Name
>> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
>> ANTIBODY 2F5 HEAVY CHAIN in water
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein_chain_P 1
>> Protein_chain_L 1
>> Protein_chain_H 1
>> SOL10
>> SOL   127
>> SOL   157
>> SOL 4177*1*
>> CL-   *8*
>> *reconstructed2 .top file*
>> ; Include topology for ions
>> #include "gromos43a1.ff/ions.itp"
>> **
>> [ system ]
>> ; Name
>> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
>> ANTIBODY 2F5 HEAVY CHAIN in water
>>
>> [ molecules ]
>> ; Compou

Re: Re: [gmx-users] total charge of the system

[Mark Abraham]

On 01/25/11, ahmet yıldırım   wrote:
> Dear Mark,
> 
> A million thanks. Problem is solved. 
> Finally,
> Select a continuous group of solvent molecules:
> ...
> Group    12 (  Water) has 126219 elements
> Group    13 (    SOL) has 126219 elements
> 
> 
> Which one should I choose 12 or 13?
> 

They're probably the same.

Mark

> 
> 
> Final topol.top file:
> 
> 
> ;    File 'topol.top' was generated
> ;    By user: onbekend (0)
> ;    On host: onbekend
> ;    At date: Tue Jan 25 10:12:14 2011
> 
> ;
> ;    This is a standalone topology file
> ;
> ;    It was generated using program:
> ;    pdb2gmx - VERSION 4.5.3
> ;
> ;    Command line was:
> ;    pdb2gmx -f 3MOA.pdb -water spc -ter 
> ;
> ;    Force field was read from the standard Gromacs share directory.
> 
> ;
> 
> ; Include forcefield parameters
> #include "gromos43a1.ff/forcefield.itp"
> 
> ; Include chain topologies
> #include "topol_Protein_chain_P.itp"
> #include "topol_Protein_chain_L.itp"
> 
> #include "topol_Protein_chain_H.itp"
> 
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> 
> ;  i funct   fcx    fcy    fcz
>    1    1   1000   1000   1000
> #endif
> 
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 
> ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL    10
> SOL   127
> SOL   157
> SOL 41771
> 
> CL         8
> 
> 
> 
> 25 Ocak 2011 13:13 tarihinde Mark Abraham  yazdı:
> 
> > 
> > 
> > 
> > On 01/25/11, ahmet yıldırım   wrote:
> > 
> > > 
> > > Dear Mark and Emanuel,
> > > 
> > > I am sending the ions.tip and the topol.top files. Everything seems ok. 
> > > Any problem about these files?
> > > 
> > > 
> > 
> > 
> > No. So one of the other #include files is erroneously defining ion molecule 
> > types. See 
> > www.gromacs.org/Documentation/Include_File_Mechanism(http://www.gromacs.org/Documentation/Include_File_Mechanism).
> >  Go and read them and fix it.
> > 
> > 
> > As the link I sent last time hinted, you need to name *molecules* in the 
> > [molecules] directive. Look carefully at the *molecule* name of chloride 
> > where it is defined.
> > 
> > Mark
> > 
> > 
> > 
> > > 
> > > 
> > > 
> > > By the way, I am using the Gromacs 4.5.3.
> > > Force Field 43a1
> > > 
> > > 25 Ocak 2011 12:03 tarihinde Emanuel Peter 
> > >  yazdı:
> > > 
> > > 
> > > 
> > > > Hello,
> > > > 
> > > > You have to look into your ions.itp which is included in your top-file 
> > > > by #include ions.itp.
> > > > 
> > > > 
> > > > There all the types of ions have to be defined.
> > > > The atom-types which you can see in the ions.itp, you will
> > > > find in the ff"your-forcefield".itp where your atomtypes are defined.
> > > > On top of your .top file the Atomtype-itp-file is included.
> > > > 
> > > > 
> > > > All these files are normally placed in /usr/share/gromacs/top/.
> > > > But you also can place them into your current directory.
> > > > 
> > > > Bests,
> > > > 
> > > > Emanuel
> > > > 
> > > > >>> Mark Abraham  25.01.11 10.48 Uhr >>>
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > On 01/25/11, ahmet yıldırım   wrote:
> > > > > 
> > > > > 
> > > > > Dear Mark,
> > > > > 
> > > > > I looked at gromacs mail list but I could not find a proper solution 
> > > > > .What should I add to the .top file? Please look at the following 
> > > > > reconstructed1 .top and reconstructed1 .top files
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > I have error as the following reconstructed1 .top file:
> > > > > 
> > > > > Fatal error:
> > > > > 
> > > > > moleculetype CU1 is redefined
> > > > > 
> > > > > 
> > > > > I have error as the following reconstructed2 .top file:
> > > > > 
> > > > > Fatal error:
> > > > > 
> > > > > No such moleculetype CL-
> > > > > 
> > > > > 
> > > > 
> > > > I don't have any knowledge of the context, so can't answer. It looks to 
> > > > me like you are mixing copies of ions.itp from multiple sources. Don't. 
> > > > Use the one for the force field you are targetting. pdb2gmx generated 
> > > > the right invocation - all you should have to do is use that by 
> > > > generating correctly-named ions. See 
> > > > http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion)
> > > > 
> > > > 
> > > > 
> > > > Mark
> > > > 
> > > > 
> > > > > Original .top file:
> > > > > ; Include topology for ions
> > > > > #include "gromos43a1.ff/ions.itp"
> > > > > 
> > > > > 
> > > > > 
> > > > > [ system ]
> > > > > ; Name
> > > > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; 
> > > > > ANTI-HIV-1 ANTIBODY 2F5

[gmx-users] Can not open file: run.xtc

[ahmet yıldırım]

Dear users,

g_rms -s em.tpr -f run.xtc
Select group for least squares fit:
Selected 2: 'Protein-H'
Select group for RMSD calculation
Selected 2: 'Protein-H'

I didn't had such a problem in other samples. But now, I have the error as
the following:

Program g_rms, VERSION 4.5.3
Source code file: gmxfio.c, line: 519

Can not open file:
run.xtc

-- 
Ahmet YILDIRIM
-- 
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[gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

[gromacs]

HI Friends,

I get the following note,

The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

I want to keep the T at 300K, so does it matter to select any thermostat method?


Another note when i use PME:

Estimate for the relative computational load of the PME mesh part: 0.97

NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

So what is the reason? I use type=PME

Is my setting proper?

Thanks
-- 
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Re: [gmx-users] Can not open file: run.xtc

[Tsjerk Wassenaar]

Hi Ahmet,

That sort of indicates that the file is not there, doesn't it?
Maybe you're not doing what you expect to be doing, or doing it somewhere else.

Cheers,

Tsjerk


2011/1/25 ahmet yıldırım :
> Dear users,
>
> g_rms -s em.tpr -f run.xtc
> Select group for least squares fit:
> Selected 2: 'Protein-H'
> Select group for RMSD calculation
> Selected 2: 'Protein-H'
>
> I didn't had such a problem in other samples. But now, I have the error as
> the following:
>
> Program g_rms, VERSION 4.5.3
> Source code file: gmxfio.c, line: 519
>
> Can not open file:
> run.xtc
>
> --
> Ahmet YILDIRIM
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

[Justin A. Lemkul]

gromacs wrote:

HI Friends,

I get the following note,

The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

I want to keep the T at 300K, so does it matter to select any thermostat 
method?




The choice of thermostat certainly does matter, otherwise you wouldn't get this 
note.  Refer to the numerous discussions in the list archive as to why one would 
or would not (usually) use the Berendsen thermostat, as well as:


http://www.gromacs.org/Documentation/Terminology/Thermostats
http://www.gromacs.org/Documentation/Terminology/Berendsen



Another note when i use PME:

Estimate for the relative computational load of the PME mesh part: 0.97

NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

So what is the reason? I use type=PME



Your combination of settings (rcoulomb, fourierspacing, and perhaps a few 
others) indicate that your simulation is going to spend an inordinate amount of 
time doing PME calculations, so your performance will suffer.  Seeing your 
entire .mdp file would be necessary if you want further guidance.


-Justin


Is my setting proper?

Thanks




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Can not open file: run.xtc

[ahmet yıldırım]

Dear Tsjerk,

Thank you. Problem solved.
g_rms -s em.tpr -f run.trr -o rmsd.xvg
xmgrace rmsd.xvg

25 Ocak 2011 14:51 tarihinde Tsjerk Wassenaar  yazdı:

> Hi Ahmet,
>
> That sort of indicates that the file is not there, doesn't it?
> Maybe you're not doing what you expect to be doing, or doing it somewhere
> else.
>
> Cheers,
>
> Tsjerk
>
>
> 2011/1/25 ahmet yıldırım :
> > Dear users,
> >
> > g_rms -s em.tpr -f run.xtc
> > Select group for least squares fit:
> > Selected 2: 'Protein-H'
> > Select group for RMSD calculation
> > Selected 2: 'Protein-H'
> >
> > I didn't had such a problem in other samples. But now, I have the error
> as
> > the following:
> >
> > Program g_rms, VERSION 4.5.3
> > Source code file: gmxfio.c, line: 519
> >
> > Can not open file:
> > run.xtc
> >
> > --
> > Ahmet YILDIRIM
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
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[gmx-users] compiling error in tools

[Jennifer Williams]

Hello

I know this is possibly an issue for the IT support at my Uni but I  
was wondering if someone could shed some light on what may have gone  
wrong so at least I can point them in the right direction.


As I am getting very small diffusion coefficients when using g_msd, I  
want to increase the number of decimal points the diffusion  
coefficient is displayed to.

In the file gmx_msd.c within src/tools I changed

 fprintf(out,"# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n",

to

 fprintf(out,"# D[%10s] = %.8f (+/- %.8f) (1e-5 cm^2/s)\n",

then, as I have always done, I just typed in make g_msd to recompile  
this tool.

I get the following error message:

src/tools> make g_msd
mpicc -DHAVE_CONFIG_H -I. -I../../src  -I../../include  
-DGMXLIBDIR=\"/home/jwillia4/GRO/share/top\"  
-I/home/jwillia4/GRO/include  -O3 -fomit-frame-pointer  
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT g_msd.o  
-MD -MP -MF .deps/g_msd.Tpo -c -o g_msd.o g_msd.c

mv -f .deps/g_msd.Tpo .deps/g_msd.Po
/bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3  
-fomit-frame-pointer -finline-functions -Wall -Wno-unused  
-funroll-all-loops  -L/home/jwillia4/GRO/lib  -lgslcblas  -o g_msd  
g_msd.o libgmxana_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la  
-lgsl -lnsl -lfftw3f -lm
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused  
-funroll-all-loops -o g_msd g_msd.o  -L/home/jwillia4/GRO/lib  
./.libs/libgmxana_mpi.a  
/home/jwillia4/GRO/gromacs-4.0.7/src/mdlib/.libs/libmd_mpi.a  
../mdlib/.libs/libmd_mpi.a  
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a  
../gmxlib/.libs/libgmx_mpi.a /home/jwillia4/GRO/lib/libgslcblas.so  
/home/jwillia4/GRO/lib/libgsl.so -lnsl  
/home/jwillia4/GRO/lib/libfftw3f.a -lm   -Wl,--rpath  
-Wl,/home/jwillia4/GRO/lib -Wl,--rpath -Wl,/home/jwillia4/GRO/lib
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): In  
function `init_par':

main.c:(.text+0xc0): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xc8): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): In  
function `init_multisystem':

main.c:(.text+0xb99): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xbd9): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xbee): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):network.c:(.text+0x15): more undefined references to `ompi_mpi_comm_world'  
follow
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In  
function `gmx_sumi_sim':

network.c:(.text+0x96): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x9b): undefined reference to `ompi_mpi_int'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In  
function `gmx_sumf_sim':

network.c:(.text+0x4e6): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x4eb): undefined reference to `ompi_mpi_float'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In  
function `gmx_sumd_sim':

network.c:(.text+0x9a6): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x9ab): undefined reference to `ompi_mpi_double'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In  
function `gmx_sumi':

network.c:(.text+0xe8f): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0xe94): undefined reference to `ompi_mpi_int'
network.c:(.text+0xec0): undefined reference to `ompi_mpi_int'
network.c:(.text+0xed7): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0xedc): undefined reference to `ompi_mpi_int'
network.c:(.text+0x12fe): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1303): undefined reference to `ompi_mpi_int'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In  
function `gmx_sumf':

network.c:(.text+0x134e): undefined reference to `ompi_mpi_float'
network.c:(.text+0x1354): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1380): undefined reference to `ompi_mpi_float'
network.c:(.text+0x1397): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x139c): undefined reference to `ompi_mpi_float'
network.c:(.text+0x183e): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1843): undefined reference to `ompi_mpi_float'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): In  
function `gmx_sumd':

network.c:(.text+0x1890): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1895): undefined reference to `ompi_mpi_double'
network.c:(.text+0x18c2): undefined reference to `ompi_mpi_double'
network.c:(.text+0x18d7): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x18dc): undefined reference to `ompi_mpi_double'
network.c:(.text+0x1d86): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1d8b): undefined reference to `ompi_mpi_double'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_m

Re: [gmx-users] compiling error in tools

[Justin A. Lemkul]

Jennifer Williams wrote:


Hello

I know this is possibly an issue for the IT support at my Uni but I was 
wondering if someone could shed some light on what may have gone wrong 
so at least I can point them in the right direction.


As I am getting very small diffusion coefficients when using g_msd, I 
want to increase the number of decimal points the diffusion coefficient 
is displayed to.

In the file gmx_msd.c within src/tools I changed

 fprintf(out,"# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n",

to

 fprintf(out,"# D[%10s] = %.8f (+/- %.8f) (1e-5 cm^2/s)\n",

then, as I have always done, I just typed in make g_msd to recompile 
this tool.

I get the following error message:

src/tools> make g_msd
mpicc -DHAVE_CONFIG_H -I. -I../../src  -I../../include 
-DGMXLIBDIR=\"/home/jwillia4/GRO/share/top\" 
-I/home/jwillia4/GRO/include  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT g_msd.o -MD 
-MP -MF .deps/g_msd.Tpo -c -o g_msd.o g_msd.c

mv -f .deps/g_msd.Tpo .deps/g_msd.Po
/bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops  -L/home/jwillia4/GRO/lib  -lgslcblas  -o g_msd 
g_msd.o libgmxana_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la 
-lgsl -lnsl -lfftw3f -lm
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
-funroll-all-loops -o g_msd g_msd.o  -L/home/jwillia4/GRO/lib 
./.libs/libgmxana_mpi.a 
/home/jwillia4/GRO/gromacs-4.0.7/src/mdlib/.libs/libmd_mpi.a 
../mdlib/.libs/libmd_mpi.a 
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a 
../gmxlib/.libs/libgmx_mpi.a /home/jwillia4/GRO/lib/libgslcblas.so 
/home/jwillia4/GRO/lib/libgsl.so -lnsl 
/home/jwillia4/GRO/lib/libfftw3f.a -lm   -Wl,--rpath 
-Wl,/home/jwillia4/GRO/lib -Wl,--rpath -Wl,/home/jwillia4/GRO/lib
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): 
In function `init_par':

main.c:(.text+0xc0): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xc8): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(main.o): 
In function `init_multisystem':

main.c:(.text+0xb99): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xbd9): undefined reference to `ompi_mpi_comm_world'
main.c:(.text+0xbee): undefined reference to `ompi_mpi_comm_world'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o):network.c:(.text+0x15): 
more undefined references to `ompi_mpi_comm_world' follow
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): 
In function `gmx_sumi_sim':

network.c:(.text+0x96): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x9b): undefined reference to `ompi_mpi_int'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): 
In function `gmx_sumf_sim':

network.c:(.text+0x4e6): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x4eb): undefined reference to `ompi_mpi_float'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): 
In function `gmx_sumd_sim':

network.c:(.text+0x9a6): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x9ab): undefined reference to `ompi_mpi_double'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): 
In function `gmx_sumi':

network.c:(.text+0xe8f): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0xe94): undefined reference to `ompi_mpi_int'
network.c:(.text+0xec0): undefined reference to `ompi_mpi_int'
network.c:(.text+0xed7): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0xedc): undefined reference to `ompi_mpi_int'
network.c:(.text+0x12fe): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1303): undefined reference to `ompi_mpi_int'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): 
In function `gmx_sumf':

network.c:(.text+0x134e): undefined reference to `ompi_mpi_float'
network.c:(.text+0x1354): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1380): undefined reference to `ompi_mpi_float'
network.c:(.text+0x1397): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x139c): undefined reference to `ompi_mpi_float'
network.c:(.text+0x183e): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1843): undefined reference to `ompi_mpi_float'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.a(network.o): 
In function `gmx_sumd':

network.c:(.text+0x1890): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1895): undefined reference to `ompi_mpi_double'
network.c:(.text+0x18c2): undefined reference to `ompi_mpi_double'
network.c:(.text+0x18d7): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x18dc): undefined reference to `ompi_mpi_double'
network.c:(.text+0x1d86): undefined reference to `ompi_mpi_op_sum'
network.c:(.text+0x1d8b): undefined reference to `ompi_mpi_double'
/home/jwillia4/GRO/gromacs-4.0.7/src/gmxlib/.libs/libgmx_mpi.

[gmx-users] dipole moment

[Olga Ivchenko]

Dear gromacs users,

I would like to ask if there is a possibility in gromacs to calculate dipole
moment between two atoms. For example one from water and another one from
ligand.


best,
Olga
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Re: [gmx-users] dipole moment

[David van der Spoel]

On 2011-01-25 14.51, Olga Ivchenko wrote:

Dear gromacs users,

I would like to ask if there is a possibility in gromacs to calculate
dipole moment between two atoms. For example one from water and another
one from ligand.


best,
Olga

If you mean the combined dipole moment of a particular water and a 
ligand then you can do it with g_dipoles and an index file.



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] segmentation fault while running eneconv

[Anna Marabotti]

Dear all,
 
I launched on my system a first simulation of 5 ns, then I prolonged it to
50 ns using 
tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr
and then 
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times, every time I relaunched
it simply doing:
mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4
 
At the end of these simulations I obtained the following files:
- md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long
- md2_50ns.xtc and .edr: files obtained by prolonging the first MD until
50ns
- md2_50ns_2.xtc and .edr: files obtained by restarting the previous
dynamics that was interrupted before 50 ns
- md2_50ns_3.xtc and .edr: same as before
- md2_50ns_4.xtc and .edr: same as before
 
After all these runs, I want to concatenate all the dynamics in order to
have a single .xtc file md_50ns_tot and a single .edr file md_50ns_tot.edr.
For the first, I used:
trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc
md2_50ns_4.xtc -o md_50ns_tot.xtc
and all worked fine: I obtained the output file with no errors (there are no
errors also in the .log files)
 
On the contrary, when I tried to do the same with eneconv:
eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr
md2_50ns_4.edr -o md_50ns_tot.edr
I obtained the following output:
 
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
Reading energy frame  1 time  100.000
Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file
Reading energy frame  0 time0.000
Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file
Reading energy frame  0 time 14900.000
Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file
Reading energy frame  0 time 27800.000
Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file
Reading energy frame  0 time 38800.000
 
Summary of files and start times used:
 
  FileStart time
-
2GH9openmod4_pH10_5ns.edr0.000
2GH9openmod4_pH10_50ns.edr0.000
2GH9openmod4_pH10_50ns_2.part0002.edr14900.000
2GH9openmod4_pH10_50ns_3.part0003.edr27800.000
2GH9openmod4_pH10_50ns_4.part0004.edr38800.000
 
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
Segmentation fault

Looking for some hints in the gmx-users list the only thing I found that
could be similar to my problem is this old message:
http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html
 
I see in the output error message that the start time for the first two
simulations is the same: could be this one the problem for my system?
However, I did use tpbconv each time to make restarts of my simulations, I
really don't know why the start time is 0.000 in the first two cases. 
Is there a problem in the results of simulations if these two simulations
have the same start time? Practically, what can I do to concatenate my .edr
files? 
 
Many thanks in advance and best regards
Anna Marabotti
 

Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabo...@isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"When a man with a gun meets a man with a pen, the man with a gun is a dead
man"
 
-- 
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Re: [gmx-users] segmentation fault while running eneconv

[Justin A. Lemkul]

Anna Marabotti wrote:

Dear all,
 
I launched on my system a first simulation of 5 ns, then I prolonged it 
to 50 ns using

tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr
and then
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times, every time I 
relaunched it simply doing:

mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4
 
At the end of these simulations I obtained the following files:

- md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long
- md2_50ns.xtc and .edr: files obtained by prolonging the first MD until 
50ns
- md2_50ns_2.xtc and .edr: files obtained by restarting the previous 
dynamics that was interrupted before 50 ns

- md2_50ns_3.xtc and .edr: same as before
- md2_50ns_4.xtc and .edr: same as before
 
After all these runs, I want to concatenate all the dynamics in order to 
have a single .xtc file md_50ns_tot and a single .edr file 
md_50ns_tot.edr. For the first, I used:
trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc 
md2_50ns_4.xtc -o md_50ns_tot.xtc
and all worked fine: I obtained the output file with no errors (there 
are no errors also in the .log files)
 
On the contrary, when I tried to do the same with eneconv:
eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr 
md2_50ns_4.edr -o md_50ns_tot.edr

I obtained the following output:
 
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file

Reading energy frame  1 time  100.000
Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file
Reading energy frame  0 time0.000
Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file
Reading energy frame  0 time 14900.000
Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file
Reading energy frame  0 time 27800.000
Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file
Reading energy frame  0 time 38800.000
 
Summary of files and start times used:
 
  FileStart time

-
2GH9openmod4_pH10_5ns.edr0.000
2GH9openmod4_pH10_50ns.edr0.000
2GH9openmod4_pH10_50ns_2.part0002.edr14900.000
2GH9openmod4_pH10_50ns_3.part0003.edr27800.000
2GH9openmod4_pH10_50ns_4.part0004.edr38800.000
 
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file

Segmentation fault
Looking for some hints in the gmx-users list the only thing I found that 
could be similar to my problem is this old message:

http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html
 


What Gromacs version are you using?  If it is not 4.5.3, then you're probably 
running into a bug regarding double precision .edr files that was fixed some 
time ago.


I see in the output error message that the start time for the first two 
simulations is the same: could be this one the problem for my system? 
However, I did use tpbconv each time to make restarts of my simulations, 
I really don't know why the start time is 0.000 in the first two cases.


Well, your commands don't agree with the output of eneconv.  The names are 
different.  Perhaps you've confused what files you think you're using, or 
otherwise attempted to append to a file and then gave it a new name.  In any 
case, gmxcheck is your friend here.


Is there a problem in the results of simulations if these two 
simulations have the same start time? Practically, what can I do to 
concatenate my .edr files?
 


Presumably, yes.  As long as the .edr files have no internal corruptions (which, 
unfortunately, is quite possible if the job frequently went down), then you 
should be able to concatenate them.  That also depends on the version of Gromacs 
you're using, if you're running into the old bug.  It's always helpful to state 
right up front which version you're using when reporting a problem.


-Justin


Many thanks in advance and best regards
Anna Marabotti
 


Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabo...@isa.cnr.it 
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"When a man with a gun meets a man with a pen, the man with a gun is a 
dead man"
 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] dipole moment

[Olga Ivchenko]

Dear David,

I mean a dipole moment between a particle atom in a ligand and a particular
atom in water molecule. G_dipoles works for molecules, as I understood, not
for atoms.

best,
Olga


2011/1/25 David van der Spoel 

> On 2011-01-25 14.51, Olga Ivchenko wrote:
>
>> Dear gromacs users,
>>
>> I would like to ask if there is a possibility in gromacs to calculate
>> dipole moment between two atoms. For example one from water and another
>> one from ligand.
>>
>>
>> best,
>> Olga
>>
>>  If you mean the combined dipole moment of a particular water and a ligand
> then you can do it with g_dipoles and an index file.
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] dipole moment

[David van der Spoel]

On 2011-01-25 16.01, Olga Ivchenko wrote:

Dear David,

I mean a dipole moment between a particle atom in a ligand and a
particular atom in water molecule. G_dipoles works for molecules, as I
understood, not for atoms.


You can measure the distance between them, the dipole moment will be 
ill-defined unless the two atoms together have a zero charge.




best,
Olga


2011/1/25 David van der Spoel mailto:sp...@xray.bmc.uu.se>>

On 2011-01-25 14.51, Olga Ivchenko wrote:

Dear gromacs users,

I would like to ask if there is a possibility in gromacs to
calculate
dipole moment between two atoms. For example one from water and
another
one from ligand.


best,
Olga

If you mean the combined dipole moment of a particular water and a
ligand then you can do it with g_dipoles and an index file.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] dipole moment

[Olga Ivchenko]

Thank you David,

Olga

2011/1/25 David van der Spoel 

> On 2011-01-25 16.01, Olga Ivchenko wrote:
>
>> Dear David,
>>
>> I mean a dipole moment between a particle atom in a ligand and a
>> particular atom in water molecule. G_dipoles works for molecules, as I
>> understood, not for atoms.
>>
>
> You can measure the distance between them, the dipole moment will be
> ill-defined unless the two atoms together have a zero charge.
>
>
>> best,
>> Olga
>>
>>
>> 2011/1/25 David van der Spoel > >
>>
>>
>>On 2011-01-25 14.51, Olga Ivchenko wrote:
>>
>>Dear gromacs users,
>>
>>I would like to ask if there is a possibility in gromacs to
>>calculate
>>dipole moment between two atoms. For example one from water and
>>another
>>one from ligand.
>>
>>
>>best,
>>Olga
>>
>>If you mean the combined dipole moment of a particular water and a
>>ligand then you can do it with g_dipoles and an index file.
>>
>>
>>--
>>David van der Spoel, Ph.D., Professor of Biology
>>Dept. of Cell & Molec. Biol., Uppsala University.
>>Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>sp...@xray.bmc.uu.se 
>>
>>http://folding.bmc.uu.se
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
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[gmx-users] Umbrella Sampling for a single molecule

[Sai Pooja]

Hi,

I am interested in carrying out umbrella sampling for a protein in explicit
solvent with the charmm forcefield. I want to impose a harmonic potential in
the dihedral space of only some specific atoms in the protein molecule. I am
having trouble figuring out a way to apply this using gromacs. Can I get
some help on this?

Thanks
Pooja

p.s. I have seen the tutorial on US by Justin but I am not sure if that is
applicable to a single molecule when the purpose is to obtain the
free-energy function associated with the transition in dihedral angles
of specific some atoms in a protein molecule

-- 
Quaerendo Invenietis-Seek and you shall discover.
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Re: [gmx-users] Umbrella Sampling for a single molecule

[Justin A. Lemkul]

Sai Pooja wrote:

Hi,
 
I am interested in carrying out umbrella sampling for a protein in 
explicit solvent with the charmm forcefield. I want to impose a harmonic 
potential in the dihedral space of only some specific atoms in the 
protein molecule. I am having trouble figuring out a way to apply this 
using gromacs. Can I get some help on this?
 


http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints

You'll have to build various configurations that correspond to different 
dihedral angles (which form the sampling windows), then restrain them.


The energy attributed to the restraints is then stored in the .edr file.  From 
these energies, you should be able to construct the energy curve over the 
sampling windows.  There are examples of this in the literature, so I suspect 
you should be able to find some demonstrations of how it's applied.


-Justin


Thanks
Pooja
 
p.s. I have seen the tutorial on US by Justin but I am not sure if that 
is applicable to a single molecule when the purpose is to obtain the 
free-energy function associated with the transition in dihedral angles 
of specific some atoms in a protein molecule


--
Quaerendo Invenietis-Seek and you shall discover.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: segmentation fault while running eneconv

[anna . marabotti]

Dear Justin,
thank you for your answer. I'm currently using Gromacs version 4.0.7
which was compiled in double precision, therefore I strongly suspect
that this is a problem linked to the old bug. It seems to me that I used
eneconv previously on this machine to concatenate .edr files, but I
cannot be sure. However, before writing you I copied the .edr files on
another machine, which still has Gromacs 4.0.7 installed, but compiled
in single precision, and still I found the same error Segmentation fault.

Concerning the name of the files, when I described the commands in my
previous message I used a "simplified" version of their names in order
to avoid writing the long 2GH9openmod4_pH...blabla, but I checked
several times the names I used and I can assure you that I tried to
concatenate the correct file names. Therefore, the problem is not a
typo. Sorry for not explaining it before.

I made a check wit gmxcheck on 2 files: the .edr and .xtc files from the
MD of 5 ns and the .edr and .xtc files from the MD of 50 ns (started
immediately after the 5ns using tpbconv): these are the results:
Checking file 2GH9openmod4_pH10_5ns.xtc
Reading frame   0 time0.000
# Atoms  40139
Precision 0.001 (nm)
Last frame   1000 time 5000.000
Item#frames Timestep (ps)
Step  10015
Time  10015
Lambda   0
Coords10015
Velocities   0
Forces   0
Box   10015

Checking energy file 2GH9openmod4_pH10_5ns.edr
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
frame:  0 (index  0), t:  0.000
Last energy frame read 50 time 5000.000
Found 51 frames with a timestep of 100 ps.

Checking file 2GH9openmod4_pH10_50ns.xtc
Reading frame   0 time0.000
# Atoms  40139
Precision 0.001 (nm)
Reading frame2000 time 1.000
Item#frames Timestep (ps)
Step  29815
Time  29815
Lambda   0
Coords29815
Velocities   0
Forces   0
Box   29815

Checking energy file 2GH9openmod4_pH10_50ns.edr
Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file
frame:  0 (index  0), t:  0.000
Last energy frame read 149 time 14900.000
Found 150 frames with a timestep of 100 ps.

It seems to me that all is regular; the only strange thing is that both
start at time 0, despite I used tpbconv+mdrun with cpi to continue the
MD after the first 5 ns.

I return with my previous question: how can I manage this problem,
especially if I have the version 4.0.7? Do I have to ask administrators
to fix the bug? Do I have to restart all my simulations?

Thank you very much and best regards
Anna

>--
>
>Message: 1
>Date: Tue, 25 Jan 2011 09:43:20 -0500
>From: "Justin A. Lemkul" 
>Subject: Re: [gmx-users] segmentation fault while running eneconv
>To: Discussion list for GROMACS users 
>Message-ID: <4d3ee188.7000...@vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>Anna Marabotti wrote:
>> Dear all,
>>
>> I launched on my system a first simulation of 5 ns, then I prolonged it
>> to 50 ns using
>> tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr
>> and then
>> mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
>> Since my simulation was interrupted several times, every time I
>> relaunched it simply doing:
>> mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4
>>
>> At the end of these simulations I obtained the following files:
>> - md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long
>> - md2_50ns.xtc and .edr: files obtained by prolonging the first MD until
>> 50ns
>> - md2_50ns_2.xtc and .edr: files obtained by restarting the previous
>> dynamics that was interrupted before 50 ns
>> - md2_50ns_3.xtc and .edr: same as before
>> - md2_50ns_4.xtc and .edr: same as before
>>
>> After all these runs, I want to concatenate all the dynamics in order to
>> have a single .xtc file md_50ns_tot and a single .edr file
>> md_50ns_tot.edr. For the first, I used:
>> trjcat -f md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc
>> md2_50ns_4.xtc -o md_50ns_tot.xtc
>> and all worked fine: I obtained the output file with no errors (there
>> are no errors also in the .log files)
>>
>> On the contrary, when I tried to do the same with eneconv:
>> eneconv -f md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr
>> md2_50ns_4.edr -o md_50ns_tot.edr
>> I obtained the following output:
>>
>> Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
>> Reading energy frame  1 time  100.000
>> Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file
>> Reading energy frame  0 time0.000
>> Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file
>> Reading energy frame  0 time 14900.000
>> Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file
>> Reading energy frame  0 time 27800.000
>> Opened 2

Re: [gmx-users] Re: Secondary structure loss in implicit solvent simulations

[Michael Shirts]

OK, that is what I was trying to figure out -- is the problem
reproducible on both GPU and CPU.  Now, you havent answered the direct
question, if the energies are the same for at least the first 5 steps
are so -- without that knowledge, then here might be different errors
occurring in GPU vs CPU.

At this point, the question is then whether this works with another
code with the same input parameters.  Sander (part of the AmberTools
system)is downloadable (I believe to anyone, not just academics), so
you can try running the same system on Sander, using the best fit to
the implicit solvent model in gromacs.

If THAT works, and Gromacs GPU fails, then it would appear to be a
problem with Gromacs implicit solvent implementation, and should be
posted to redmine as a bug, as well as described on the list with full
details (more than you have provided so far!) so that it can be
reproduced by the developers.

Best,

On Tue, Jan 25, 2011 at 5:05 AM, K. Singhal  wrote:
> Hi
>
> It's not necessarily GPU-specific, it's implicit solvent-specific. I don't 
> get these problems in explicit solvent simulations on CPU, only in implicit 
> solvent simulations both on GPU as well as CPU. One of the problems that I 
> can think of is unbalanced charges that I would have balanced out using NaCl 
> ions, but not any more.
>
> Regards
> Kush
>
>
>
> --
> Kushagra Singhal
> Promovendus, Computational Chemistry
> van 't Hoff Institute of Molecular Sciences
> Science Park 904, room C2.119
> 1098 XH Amsterdam, The Netherlands
> +31 205256965
> Universiteit van Amsterdam
> k.sing...@uva.nl
>
>
> --
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Re: [gmx-users] Re: segmentation fault while running eneconv

[Justin A. Lemkul]

anna.marabo...@isa.cnr.it wrote:

Dear Justin,
thank you for your answer. I'm currently using Gromacs version 4.0.7
which was compiled in double precision, therefore I strongly suspect
that this is a problem linked to the old bug. It seems to me that I used
eneconv previously on this machine to concatenate .edr files, but I
cannot be sure. However, before writing you I copied the .edr files on
another machine, which still has Gromacs 4.0.7 installed, but compiled
in single precision, and still I found the same error Segmentation fault.



I don't believe you have a problem related to the bug; it was introduced in the 
4.5 series, so 4.0.7 should be unaffected.  Since gmxcheck seems to have worked, 
that's more evidence that there is no bug.  The problem was in the .edr 
formating, causing all Gromacs utilities to stop reading double-precision .edr 
files.



Concerning the name of the files, when I described the commands in my
previous message I used a "simplified" version of their names in order
to avoid writing the long 2GH9openmod4_pH...blabla, but I checked
several times the names I used and I can assure you that I tried to
concatenate the correct file names. Therefore, the problem is not a
typo. Sorry for not explaining it before.



OK.  Literal is always better, and often requires a simple cut and paste from 
the terminal, rather than any manual typing at all :)



I made a check wit gmxcheck on 2 files: the .edr and .xtc files from the
MD of 5 ns and the .edr and .xtc files from the MD of 50 ns (started
immediately after the 5ns using tpbconv): these are the results:
Checking file 2GH9openmod4_pH10_5ns.xtc
Reading frame   0 time0.000
# Atoms  40139
Precision 0.001 (nm)
Last frame   1000 time 5000.000
Item#frames Timestep (ps)
Step  10015
Time  10015
Lambda   0
Coords10015
Velocities   0
Forces   0
Box   10015

Checking energy file 2GH9openmod4_pH10_5ns.edr
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
frame:  0 (index  0), t:  0.000
Last energy frame read 50 time 5000.000
Found 51 frames with a timestep of 100 ps.

Checking file 2GH9openmod4_pH10_50ns.xtc
Reading frame   0 time0.000
# Atoms  40139
Precision 0.001 (nm)
Reading frame2000 time 1.000
Item#frames Timestep (ps)
Step  29815
Time  29815
Lambda   0
Coords29815
Velocities   0
Forces   0
Box   29815

Checking energy file 2GH9openmod4_pH10_50ns.edr
Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file
frame:  0 (index  0), t:  0.000
Last energy frame read 149 time 14900.000
Found 150 frames with a timestep of 100 ps.

It seems to me that all is regular; the only strange thing is that both
start at time 0, despite I used tpbconv+mdrun with cpi to continue the
MD after the first 5 ns.



What does the log file tell you regarding the outset of the second job?  It 
should say that it's starting from a checkpoint, and the first interval written 
should have a time of 5000 ps.  If not, then the checkpoint file was not 
properly used.  If both .edr files start at the same point, that could be a 
reason for the seg fault, but that's a bit of a guess.


From the gmxcheck output, it appears that your _50ns.edr file does indeed start 
from 0 instead of 5000, as you would hope.



I return with my previous question: how can I manage this problem,
especially if I have the version 4.0.7? Do I have to ask administrators
to fix the bug? Do I have to restart all my simulations?



If the "continuation" instead started from t=0, then you don't have to re-do 
anything, just don't use the _5ns.* information (.xtc, .edr, etc) since you 
basically did that portion of the simulation over.  The log files will tell you 
what's going on.


-Justin


Thank you very much and best regards
Anna


--

Message: 1
Date: Tue, 25 Jan 2011 09:43:20 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] segmentation fault while running eneconv
To: Discussion list for GROMACS users 
Message-ID: <4d3ee188.7000...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Anna Marabotti wrote:

Dear all,

I launched on my system a first simulation of 5 ns, then I prolonged it
to 50 ns using
tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr
and then
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times, every time I
relaunched it simply doing:
mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4

At the end of these simulations I obtained the following files:
- md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long
- md2_50ns.xtc and .edr: files obtained by prolonging the first MD until
50ns
- md2_50ns_2.xtc and .edr: files obtained by restarting the previous
dynamics that was interrupted b

[gmx-users] Two machines, same job, one fails

[TJ Mustard]

  

  
Hi all,

 

I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2.

 

My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H)

 

Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors)

 

We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it.

 

What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines.

 

Below is my command sequence:

 

echo ==
date >>RNAP-C.joblog
echo g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o RNAP-C_em.tpr
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o RNAP-C_em.tpr
date >>RNAP-C.joblog
echo g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g emlog.log -cpo state_em.cpt -nt 2
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g emlog.log -cpo stat_em.cpt -nt 2
date >>RNAP-C.joblog
echo g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top -o RNAP-C_pr.tpr
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top -o RNAP-C_pr.tpr
echo g453s-mdrun -v -s RNAP-C_pr.tpr -e pr.edr -c RNAP-C_after_pr.gro -g prlog.log -cpo state_pr.cpt -nt 2 -dhdl dhdl-pr.xvg
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_pr.tpr -e pr.edr -c RNAP-C_after_pr.gro -g prlog.log -cpo state_pr.cpt -nt 2 -dhdl dhdl-pr.xvg
date >>RNAP-C.joblog
echo g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top -o RNAP-C_md.tpr
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top -o RNAP-C_md.tpr
date >>RNAP-C.joblog
echo g453s-mdrun -v -s RNAP-C_md.tpr -o RNAP-C_md.trr -c RNAP-C_after_md.gro -g md.log -e md.edr -cpo state_md.cpt -nt 2 -dhdl dhdl-md.xvg
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_md.tpr -o RNAP-C_md.trr -c RNAP-C_after_md.gro -g md.log -e md.edr -cpo state_md.cpt -nt 2 -dhdl dhdl-md.xvg
date >>RNAP-C.joblog
echo g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p RNAP-C.top -o RNAP-C_fep.tpr
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p RNAP-C.top -o RNAP-C_fep.tpr
date >>RNAP-C.joblog
echo g453s-mdrun -v -s RNAP-C_fep.tpr -o RNAP-C_fep.trr -c RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_fep.tpr -o RNAP-C_fep.trr -c RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg

 

 

I can add my .mdps but I do not think they are the problem since I know it works on my personal iMac.

 

Thank you,

TJ Mustard
Email: musta...@onid.orst.edu
  

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[gmx-users] nstcomm nstcalcenergy defeats the purpose of nstcalcenergy

[ahmet yıldırım]

Dear users,

How can I fixed the NOTE the following? Will this note/warning cause a
problem in the calculations?What is the meaning of this note?

NOTE 1 [file pr.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


-- 
Ahmet YILDIRIM
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Re: [gmx-users] mdrun_mpi executable not found

[Justin Kat]

Alright. So meaning I should have instead issued:

./configure --enable-mpi --program-suffix=_mpi

make mdrun

make install-mdrun

make links


to have installed an MPI-enabled executable called mdrun_mpi apart from the
existing mdrun executable? (Would I also need to append the _mpi suffix when
issuing the first two make and make install commands above?

Thanks,
Justin

On Mon, Jan 24, 2011 at 8:08 PM, Justin A. Lemkul  wrote:

>
>
> Justin Kat wrote:
> > Thank you for the reply!
> >
> > hmm mdrun_mpi does not appear in the list of executables in
> > /usr/local/gromacs/bin (and well therefore not in /usr/local/bin).
> >
> > Which set of installation commands that I used should have compiled the
> > mdrun_mpi executable? And how should I go about getting the mdrun_mpi
> > executable at this point?
> >
>
> I see it now.  When you configured with --enable-mpi, you didn't specify
> --program-suffix=_mpi, so the installation procedure over-wrote your
> existing
> (serial) mdrun with an MPI-enabled one simply called "mdrun."  The
> configure
> output should have warned you about this.  You could, in theory, simply
> re-name
> your existing executable "mdrun_mpi" and then re-install a serial mdrun, if
> you
> need it.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
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Re: [gmx-users] nstcomm nstcalcenergy defeats the purpose of nstcalcenergy

[Mark Abraham]

On 26/01/2011 8:10 AM, ahmet yıldırım wrote:

Dear users,

How can I fixed the NOTE the following? Will this note/warning cause a 
problem in the calculations?What is the meaning of this note?


NOTE 1 [file pr.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


Did you look these definitions up in the manual before firing off an 
email? :-)


Mark
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Re: [gmx-users] mdrun_mpi executable not found

[Mark Abraham]

On 26/01/2011 8:50 AM, Justin Kat wrote:

Alright. So meaning I should have instead issued:

./configure --enable-mpi --program-suffix=_mpi||
make mdrun
make install-mdrun
make links

to have installed an MPI-enabled executable called mdrun_mpi apart 
from the existing mdrun executable? (Would I also need to append the 
_mpi suffix when issuing the first two make and make install commands 
above?


No. See http://www.gromacs.org/Downloads/Installation_Instructions

Mark



Thanks,
Justin

On Mon, Jan 24, 2011 at 8:08 PM, Justin A. Lemkul > wrote:




Justin Kat wrote:
> Thank you for the reply!
>
> hmm mdrun_mpi does not appear in the list of executables in
> /usr/local/gromacs/bin (and well therefore not in /usr/local/bin).
>
> Which set of installation commands that I used should have
compiled the
> mdrun_mpi executable? And how should I go about getting the
mdrun_mpi
> executable at this point?
>

I see it now.  When you configured with --enable-mpi, you didn't
specify
--program-suffix=_mpi, so the installation procedure over-wrote
your existing
(serial) mdrun with an MPI-enabled one simply called "mdrun."  The
configure
output should have warned you about this.  You could, in theory,
simply re-name
your existing executable "mdrun_mpi" and then re-install a serial
mdrun, if you
need it.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

[Mark Abraham]

On 26/01/2011 12:05 AM, Justin A. Lemkul wrote:



gromacs wrote:

HI Friends,

I get the following note,

The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale 
thermostat.


I want to keep the T at 300K, so does it matter to select any 
thermostat method?




The choice of thermostat certainly does matter, otherwise you wouldn't 
get this note.  Refer to the numerous discussions in the list archive 
as to why one would or would not (usually) use the Berendsen 
thermostat, as well as:


http://www.gromacs.org/Documentation/Terminology/Thermostats
http://www.gromacs.org/Documentation/Terminology/Berendsen


... and the relevant manual sections.

Mark





Another note when i use PME:

Estimate for the relative computational load of the PME mesh part: 0.97

NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

So what is the reason? I use type=PME



Your combination of settings (rcoulomb, fourierspacing, and perhaps a 
few others) indicate that your simulation is going to spend an 
inordinate amount of time doing PME calculations, so your performance 
will suffer.  Seeing your entire .mdp file would be necessary if you 
want further guidance.


-Justin


Is my setting proper?

Thanks






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Re: [gmx-users] Two machines, same job, one fails

[Mark Abraham]

On 26/01/2011 5:50 AM, TJ Mustard wrote:


Hi all,

I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and 
FFTW 3.2.2.


My iMac will run the job (over 4000 steps, till I killed it) at 4fs 
steps. (I am using heavy H)


Once I put this on our groups AMD Cluster the jobs fail even with 2fs 
steps. (with thousands of lincs errors)


We have recompiled the clusters gromacs 4.5.3 build, with no change. I 
know the system is the same since I copied the job from the server to 
my machine, to rerun it.


What is going on? Why can one machine run a job perfectly and the 
other cannot? I also know there is adequate memory on both machines.




You've posted this before, and I made a number of diagnostic 
suggestions. What did you learn?


Mark


Below is my command sequence:

echo 
==

date >>RNAP-C.joblog
echo g453s-grompp -f em.mdp -c RNAP-C_b4em.gro -p RNAP-C.top -o 
RNAP-C_em.tpr
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f em.mdp -c 
RNAP-C_b4em.gro -p RNAP-C.top -o RNAP-C_em.tpr

date >>RNAP-C.joblog
echo g453s-mdrun -v -s RNAP-C_em.tpr -c RNAP-C_after_em.gro -g 
emlog.log -cpo state_em.cpt -nt 2
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_em.tpr 
-c RNAP-C_after_em.gro -g emlog.log -cpo stat_em.cpt -nt 2

date >>RNAP-C.joblog
echo g453s-grompp -f pr.mdp -c RNAP-C_after_em.gro -p RNAP-C.top -o 
RNAP-C_pr.tpr
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f pr.mdp -c 
RNAP-C_after_em.gro -p RNAP-C.top -o RNAP-C_pr.tpr
echo g453s-mdrun -v -s RNAP-C_pr.tpr -e pr.edr -c RNAP-C_after_pr.gro 
-g prlog.log -cpo state_pr.cpt -nt 2 -dhdl dhdl-pr.xvg
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_pr.tpr 
-e pr.edr -c RNAP-C_after_pr.gro -g prlog.log -cpo state_pr.cpt -nt 2 
-dhdl dhdl-pr.xvg

date >>RNAP-C.joblog
echo g453s-grompp -f md.mdp -c RNAP-C_after_pr.gro -p RNAP-C.top -o 
RNAP-C_md.tpr
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f md.mdp -c 
RNAP-C_after_pr.gro -p RNAP-C.top -o RNAP-C_md.tpr

date >>RNAP-C.joblog
echo g453s-mdrun -v -s RNAP-C_md.tpr -o RNAP-C_md.trr -c 
RNAP-C_after_md.gro -g md.log -e md.edr -cpo state_md.cpt -nt 2 -dhdl 
dhdl-md.xvg
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_md.tpr 
-o RNAP-C_md.trr -c RNAP-C_after_md.gro -g md.log -e md.edr -cpo 
state_md.cpt -nt 2 -dhdl dhdl-md.xvg

date >>RNAP-C.joblog
echo g453s-grompp -f FEP.mdp -c RNAP-C_after_md.gro -p RNAP-C.top -o 
RNAP-C_fep.tpr
/share/apps/gromacs-4.5.3-single/bin/g453s-grompp -f FEP.mdp -c 
RNAP-C_after_md.gro -p RNAP-C.top -o RNAP-C_fep.tpr

date >>RNAP-C.joblog
echo g453s-mdrun -v -s RNAP-C_fep.tpr -o RNAP-C_fep.trr -c 
RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo state_fep.cpt -nt 2 
-dhdl dhdl-fep.xvg
/share/apps/gromacs-4.5.3-single/bin/g453s-mdrun -v -s RNAP-C_fep.tpr 
-o RNAP-C_fep.trr -c RNAP-C_after_fep.gro -g fep.log -e fep.edr -cpo 
state_fep.cpt -nt 2 -dhdl dhdl-fep.xvg


I can add my .mdps but I do not think they are the problem since I 
know it works on my personal iMac.


Thank you,

TJ Mustard
Email: musta...@onid.orst.edu



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Re: [gmx-users] Two machines, same job, one fails

[TJ Mustard]

  

  
 


  
   On January 25, 2011 at 2:08 PM Mark Abraham  wrote:
  

  
On 26/01/2011 5:50 AM, TJ Mustard wrote: 


  Hi all,

   

  I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and FFTW 3.2.2.

   

  My iMac will run the job (over 4000 steps, till I killed it) at 4fs steps. (I am using heavy H)

   

  Once I put this on our groups AMD Cluster the jobs fail even with 2fs steps. (with thousands of lincs errors)

   

  We have recompiled the clusters gromacs 4.5.3 build, with no change. I know the system is the same since I copied the job from the server to my machine, to rerun it.

   

  What is going on? Why can one machine run a job perfectly and the other cannot? I also know there is adequate memory on both machines.

 You've posted this before, and I made a number of diagnostic suggestions. What did you learn?

 Mark
  


Mark and all,

 

First thank you for all our help. What you suggested last time helped considerably with our jobs/calculations. I have learned that using the standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel) and have made these my new standard for future jobs. We chose to use the smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we understand why we need these standard settings. Now what I see to be our problem is that our machines have some sort of variable we cannot account for. If I am blind to my error, please show me. I just don't understand why one computer works while the other does not. We have recompiled gromacs 4.5.3 single precission on our cluster, and still have this problem.

 

Now I understand that my iMac works, but it only has 2 cpus and the cluster has 320. Since we are running our jobs via a Bennet's Acceptance Ratio FEP with 21 lambda windows, using just one 2 cpu machine would take too long. Especially since we wish to start pseudo high throughput drug testing.

 

 

In my .mdp files now, the only changes are:

(the default setting is on the right of the ";")

 

 

define   =     ; =

; RUN CONTROL PARAMETERS
integrator   = sd    ; = md
; Start time and timestep in ps
tinit    = 0    ; = 0
dt   = 0.004    ; = 0.001
nsteps   = 75       ; = 0 (this one depends on the window and particular part of our job)

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 1    ; = 100 (to save on disk space)
nstvout  = 1    ; = 100

 

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME    ; = Cutoff
rcoulomb-switch  = 0    ; = 0
rcoulomb = 1  ; = 1
; Relative dielectric constant for the medium and the reaction field
epsilon_r    = 1    ; = 1
epsilon_rf   = 1    ; = 1
; Method for doing Van der Waals
vdw-type = Cut-off    ; = Cut-off
; cut-off lengths   
rvdw-switch  = 0    ; = 0
rvdw = 1  ; = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12    ; = 0.12
; EWALD/PME/PPPM parameters
pme_order    = 4    ; = 4
ewald_rtol   = 1e-05    ; = 1e-05
ewald_geometry   = 3d    ; = 3d
epsilon_surface  = 0    ; = 0
optimize_fft = yes    ; = no

 

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
tcoupl   = v-rescale    ; = No
nsttcouple   = -1    ; = -1
nh-chain-length  = 10    ; = 10
; Groups to couple separately
tc-grps  = System    ; =
; Time constant (ps) and reference temperature (K)
tau-t    = 0.1    ; =
ref-t    = 300    ; =
; Pressure coupling     
Pcoupl   = Parrinello-Rahman    ; = No
Pcoupltype   = Isotropic
nstpcouple   = -1    ; = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p    = 1    ; = 1
compressibility  = 4.5e-5    ; =
ref-p    = 1.0    ; =

 

; OPTIONS FOR BONDS    
constraints  = all-bonds    ; = none
; Type of constraint algorithm
constraint-algorithm = Lincs    ; = Lincs

 

; Free energy control stuff
free-energy  = yes    ; = no
init-lambda  = 0.00       ; = 0
delta-lambda = 0    ; = 0
foreign_lambda   =        0.05 ; =
sc-alpha = 0.5    ; = 0
sc-power   

Re: [gmx-users] Two machines, same job, one fails

[Justin A. Lemkul]

TJ Mustard wrote:



 



On January 25, 2011 at 2:08 PM Mark Abraham  wrote:


On 26/01/2011 5:50 AM, TJ Mustard wrote:


Hi all,

 

I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and 
FFTW 3.2.2.


 

My iMac will run the job (over 4000 steps, till I killed it) at 4fs 
steps. (I am using heavy H)


 

Once I put this on our groups AMD Cluster the jobs fail even with 2fs 
steps. (with thousands of lincs errors)


 

We have recompiled the clusters gromacs 4.5.3 build, with no change. 
I know the system is the same since I copied the job from the server 
to my machine, to rerun it.


 

What is going on? Why can one machine run a job perfectly and the 
other cannot? I also know there is adequate memory on both machines.




You've posted this before, and I made a number of diagnostic 
suggestions. What did you learn?


Mark


Mark and all,

 

First thank you for all our help. What you suggested last time helped 
considerably with our jobs/calculations. I have learned that using the 
standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel) 
and have made these my new standard for future jobs. We chose to use the 
smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we 
understand why we need these standard settings. Now what I see to be our 
problem is that our machines have some sort of variable we cannot 
account for. If I am blind to my error, please show me. I just don't 
understand why one computer works while the other does not. We have 
recompiled gromacs 4.5.3 single precission on our cluster, and still 
have this problem.




I know the feeling all too well.  PowerPC jobs crash instantly, on our cluster, 
despite working beautifully on our lab machines.  There's a bug report about 
that one, but I haven't heard anything about AMD failures.  It remains a 
possibility that something beyond your control is going on.  To explore a bit 
further:


1. Do the systems in question crash immediately (i.e., step zero) or do they run 
for some time?


2. If they give you even a little bit of output, you can analyze which energy 
terms, etc go haywire with the tips listed here:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

That would help in tracking down any potential bug or error.

3. Is it just the production runs that are crashing, or everything?  If EM isn't 
even working, that smells even buggier.


4. Are the compilers the same on the iMac vs. AMD cluster?

-Justin

 

Now I understand that my iMac works, but it only has 2 cpus and the 
cluster has 320. Since we are running our jobs via a Bennet's Acceptance 
Ratio FEP with 21 lambda windows, using just one 2 cpu machine would 
take too long. Especially since we wish to start pseudo high throughput 
drug testing.


 

 


In my .mdp files now, the only changes are:

(the default setting is on the right of the ";")

 

 


define   = ; =

; RUN CONTROL PARAMETERS
integrator   = sd; = md
; Start time and timestep in ps
tinit= 0; = 0
dt   = 0.004; = 0.001
nsteps   = 75   ; = 0 (this one depends on the 
window and particular part of our job)


; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 1; = 100 (to save on disk space)
nstvout  = 1; = 100

 


; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME; = Cutoff
rcoulomb-switch  = 0; = 0
rcoulomb = 1  ; = 1
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1; = 1
epsilon_rf   = 1; = 1
; Method for doing Van der Waals
vdw-type = Cut-off; = Cut-off
; cut-off lengths   
rvdw-switch  = 0; = 0

rvdw = 1  ; = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12; = 0.12
; EWALD/PME/PPPM parameters
pme_order= 4; = 4
ewald_rtol   = 1e-05; = 1e-05
ewald_geometry   = 3d; = 3d
epsilon_surface  = 0; = 0
optimize_fft = yes; = no

 


; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
tcoupl   = v-rescale; = No

nsttcouple   = -1; = -1
nh-chain-length  = 10; = 10
; Groups to couple separately
tc-grps  = System; =
; Time constant (ps) and reference temperature (K)
tau-t= 0.1; =
ref-t= 300; =
; Pressure coupling 
Pcoupl   = Parrinello-Rahman; = No

Pcoupltype   = Isotropic
nstpcouple   = -1; = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 1; = 1
compressibility  = 4.5e-5; =
ref-p

[gmx-users] (no subject)

[trevor brown]

Dear Justin/Mark,
I would like to have a private course about Gromacs in Holland.
Is there such a facility for this? Who should I talk with?

Or is there a workshop in near future?
best wishes
-- 
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Re: [gmx-users] Two machines, same job, one fails

[TJ Mustard]

  

  
 


  On January 25, 2011 at 3:24 PM "Justin A. Lemkul"  wrote:
  
  >
  >
  > TJ Mustard wrote:
  > >
  > >
  > > 
  > >
  > >
  > > On January 25, 2011 at 2:08 PM Mark Abraham  wrote:
  > >
  > >> On 26/01/2011 5:50 AM, TJ Mustard wrote:
  > >>>
  > >>> Hi all,
  > >>>
  > >>> 
  > >>>
  > >>> I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and
  > >>> FFTW 3.2.2.
  > >>>
  > >>> 
  > >>>
  > >>> My iMac will run the job (over 4000 steps, till I killed it) at 4fs
  > >>> steps. (I am using heavy H)
  > >>>
  > >>> 
  > >>>
  > >>> Once I put this on our groups AMD Cluster the jobs fail even with 2fs
  > >>> steps. (with thousands of lincs errors)
  > >>>
  > >>> 
  > >>>
  > >>> We have recompiled the clusters gromacs 4.5.3 build, with no change.
  > >>> I know the system is the same since I copied the job from the server
  > >>> to my machine, to rerun it.
  > >>>
  > >>> 
  > >>>
  > >>> What is going on? Why can one machine run a job perfectly and the
  > >>> other cannot? I also know there is adequate memory on both machines.
  > >>>
  > >>
  > >> You've posted this before, and I made a number of diagnostic
  > >> suggestions. What did you learn?
  > >>
  > >> Mark
  > >
  > > Mark and all,
  > >
  > > 
  > >
  > > First thank you for all our help. What you suggested last time helped
  > > considerably with our jobs/calculations. I have learned that using the
  > > standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel)
  > > and have made these my new standard for future jobs. We chose to use the
  > > smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we
  > > understand why we need these standard settings. Now what I see to be our
  > > problem is that our machines have some sort of variable we cannot
  > > account for. If I am blind to my error, please show me. I just don't
  > > understand why one computer works while the other does not. We have
  > > recompiled gromacs 4.5.3 single precission on our cluster, and still
  > > have this problem.
  > >
  >
  > I know the feeling all too well.  PowerPC jobs crash instantly, on our cluster,
  > despite working beautifully on our lab machines.  There's a bug report about
  > that one, but I haven't heard anything about AMD failures.  It remains a
  > possibility that something beyond your control is going on.  To explore a bit
  > further:
  >
  > 1. Do the systems in question crash immediately (i.e., step zero) or do they run
  > for some time?
  >


Step 0, every time.

 


  > 2. If they give you even a little bit of output, you can analyze which energy
  > terms, etc go haywire with the tips listed here:
  >


All I have seen on these is LINCS Errors and Water molecules unable to be settled.

 

But I will check this out right now, and email if I smell trouble.

 


  > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
  >
  > That would help in tracking down any potential bug or error.
  >
  > 3. Is it just the production runs that are crashing, or everything?  If EM isn't
  > even working, that smells even buggier.


Awesome question here, we have seen some weird stuff. Sometimes the cluster will give us segmentation faults, then it will fail on our machines or sometimes not on our iMacs. I know weird! If EM starts on the cluster it will finish. Where we have issues is in positional restraint (PR) and MD and MD/FEP. It doesn't matter if FEP is on or off in a MD (although we are using SD for these MD/FEP runs).

 


  >
  > 4. Are the compilers the same on the iMac vs. AMD cluster?


No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using x86_64-redhat-linux 4.1.2 GCC.

I just did a quick yum search and there doesn't seem to be a newer GCC. We know you are going to cmake but we have yet to get it implemented on our cluster successfully.

 

Thank you,

TJ Mustard

 


  >
  > -Justin
  >
  > > 
  > >
  > > Now I understand that my iMac works, but it only has 2 cpus and the
  > > cluster has 320. Since we are running our jobs via a Bennet's Acceptance
  > > Ratio FEP with 21 lambda windows, using just one 2 cpu machine would
  > > take too long. Especially since we wish to start pseudo high throughput
  > > drug testing.
  > >
  > > 
  > >
  > > 
  > >
  > > In my .mdp files now, the only changes are:
  > >
  > > (the default setting is on the right of the ";")
  > >
  > > 
  > >
  > > 
  > >
  > > define         

Re: [gmx-users] Need help troubleshooting an mdrun-gpu error message!

[Szilárd Páll]

Hi,

There are two things you should test:

a) Does your NVIDIA driver + CUDA setup work? Try to run a different
CUDA-based program, e.g. you can get the CUDA SDK and compile one of
the simple programs like deviceQuery or bandwidthTest.

b) If the above works, try to compile OpenMM from source with the same
CUDA version as the one used when compiling Gromacs.

Let me know if you succeed!

Cheers,
--
Szilárd



On Tue, Jan 25, 2011 at 3:49 AM, Solomon Berman  wrote:
> Hello friends,
> I have installed mdrun-gpu v. 4.5.3 without incident on my group's computer
> with a suitable GPU.  The computer uses a Linux OS.  CUDA and OpenMM are
> installed in the usual places.  I created the topol.tpr file with grompp v.
> 4.5.3, also without incident.  When I run ./mdrun-gpu -v, the following
> error message is produced:
> Program mdrun-gpu, VERSION 4.5.3
> Source code file:
> /home/smberman/sourcecode/gromacs-4.5.3/src/kernel/openmm_wrapper.cpp, line:
> 1259
> Fatal error:
> The requested platform "CUDA" could not be found.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> I have the following in my .bash_profile:
> export PATH=~/bin:~/usr/bin:~/usr/local/bin:/usr/local/cuda/bin:$PATH:.
> LD_LIBRARY_PATH="/usr/local/openmm/lib:/usr/local/cuda/lib"
> export LD_LIBRARY_PATH
> I have run the available tests that came with the OpenMM library, and the
> CUDA tests pass.
> Could someone please explain what this error means and the appropriate way
> to remedy it?  Thank you!!
> Best,
> Solomon Berman
> Chemistry Department
> Boston University
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
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Please search the archive at 
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Re: [gmx-users] Two machines, same job, one fails

[Mark Abraham]

On 01/26/11, TJ Mustard   wrote:
> 
> 
> 
> 
>   
> 
> 
>   
> 
> 
> 
> 
> 
>  
> 
> 
> 
>   On January 25, 2011 at 3:24 PM "Justin A. Lemkul"  
> wrote:
> 
>   
> 
>   >
> 
>   >
> 
>   > TJ Mustard wrote:
> 
>   > >
> 
>   > >
> 
>   > > 
> 
>   > >
> 
>   > >
> 
>   > > On January 25, 2011 at 2:08 PM Mark Abraham 
>  wrote:
> 
>   > >
> 
>   > >> On 26/01/2011 5:50 AM, TJ Mustard wrote:
> 
>   > >>>
> 
>   > >>> Hi all,
> 
>   > >>>
> 
>   > >>> 
> 
>   > >>>
> 
>   > >>> I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 
> and
> 
>   > >>> FFTW 3.2.2.
> 
>   > >>>
> 
>   > >>> 
> 
>   > >>>
> 
>   > >>> My iMac will run the job (over 4000 steps, till I killed it) at 
> 4fs
> 
>   > >>> steps. (I am using heavy H)
> 
>   > >>>
> 
>   > >>> 
> 
>   > >>>
> 
>   > >>> Once I put this on our groups AMD Cluster the jobs fail even with 
> 2fs
> 
>   > >>> steps. (with thousands of lincs errors)
> 
>   > >>>
> 
>   > >>> 
> 
>   > >>>
> 
>   > >>> We have recompiled the clusters gromacs 4.5.3 build, with no 
> change.
> 
>   > >>> I know the system is the same since I copied the job from the 
> server
> 
>   > >>> to my machine, to rerun it.
> 
>   > >>>
> 
>   > >>> 
> 
>   > >>>
> 
>   > >>> What is going on? Why can one machine run a job perfectly and the
> 
>   > >>> other cannot? I also know there is adequate memory on both 
> machines.
> 
>   > >>>
> 
>   > >>
> 
>   > >> You've posted this before, and I made a number of diagnostic
> 
>   > >> suggestions. What did you learn?
> 
>   > >>
> 
>   > >> Mark
> 
>   > >
> 
>   > > Mark and all,
> 
>   > >
> 
>   > > 
> 
>   > >
> 
>   > > First thank you for all our help. What you suggested last time 
> helped
> 
>   > > considerably with our jobs/calculations. I have learned that using 
> the
> 
>   > > standard mdp settings allow my heavyh 4fs jobs to run on my iMac 
> (intel)
> 
>   > > and have made these my new standard for future jobs. We chose to 
> use the
> 
>   > > smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we
> 
>   > > understand why we need these standard settings. Now what I see to 
> be our
> 
>   > > problem is that our machines have some sort of variable we cannot
> 
>   > > account for. If I am blind to my error, please show me. I just don't
> 
>   > > understand why one computer works while the other does not. We have
> 
>   > > recompiled gromacs 4.5.3 single precission on our cluster, and still
> 
>   > > have this problem.
> 
>   > >
> 
>   >
> 
>   > I know the feeling all too well.  PowerPC jobs crash instantly, on 
> our cluster,
> 
>   > despite working beautifully on our lab machines.  There's a bug 
> report about
> 
>   > that one, but I haven't heard anything about AMD failures.  It 
> remains a
> 
>   > possibility that something beyond your control is going on.  To 
> explore a bit
> 
>   > further:
> 
>   >
> 
>   > 1. Do the systems in question crash immediately (i.e., step zero) or 
> do they run
> 
>   > for some time?
> 
>   >
> 
> 
> 
> 
> Step 0, every time.
> 
> 
> 
>  
> 
> 
> 
>   > 2. If they give you even a little bit of output, you can analyze 
> which energy
> 
>   > terms, etc go haywire with the tips listed here:
> 
>   >
> 
> 
> 
> 
> All I have seen on these is LINCS Errors and Water molecules unable to be 
> settled.
> 
> 
> 
>  
> 
> 
> 
> But I will check this out right now, and email if I smell trouble.
> 
> 
> 
>  
> 
> 
> 
>   > 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
> 
>   >
> 
>   > That would help in tracking down any potential bug or error.
> 
>   >
> 
>   > 3. Is it just the production runs that are crashing, or everything?  
> If EM isn't
> 
>   > even working, that smells even buggier.
> 
> 
> 
> 
> Awesome question here, we have seen some weird stuff. Sometimes the cluster 
> will give us segmentation faults, then it will fail on our machines or 
> sometimes not on our iMacs. I know weird! If EM starts on the cluster it will 
> finish. Where we have issues is in positional restraint (PR) and MD and 
> MD/FEP. It doesn't matter if FEP is on or off in a MD (although we are using 
> SD for these MD/FEP runs).
> 
> 
> 
> 
> 
> 
Good. That rules out FEP as the source of the problem, like I asked in your 
previous thread.
 
> 
> 
> 
> 
> 
> 
>   >
> 
>   > 4. Are the compilers the same on the iMac vs. AMD cluster?
> 
> 
> 
> 
> No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using 
> x86_64-redhat-linux 4.1.2 GCC.
> 
> 
> 
> I just did a quick yum search and there 
> doesn't s

Re: [gmx-users] Two machines, same job, one fails

[Justin A. Lemkul]

TJ Mustard wrote:



 > 1. Do the systems in question crash immediately (i.e., step zero) or 
do they run

 > for some time?
 >

Step 0, every time.

 

 > 2. If they give you even a little bit of output, you can analyze 
which energy

 > terms, etc go haywire with the tips listed here:
 >

All I have seen on these is LINCS Errors and Water molecules unable to 
be settled.


 


But I will check this out right now, and email if I smell trouble.

 

 > 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

 >
 > That would help in tracking down any potential bug or error.
 >
 > 3. Is it just the production runs that are crashing, or everything?  
If EM isn't

 > even working, that smells even buggier.

Awesome question here, we have seen some weird stuff. Sometimes the 
cluster will give us segmentation faults, then it will fail on our 
machines or sometimes not on our iMacs. I know weird! If EM starts on 
the cluster it will finish. Where we have issues is in positional 
restraint (PR) and MD and MD/FEP. It doesn't matter if FEP is on or off 
in a MD (although we are using SD for these MD/FEP runs).


 


Does "sometimes" refer to different simulations, or multiple invocations of the 
same simulation system?  If you're referencing the fact that system A works 
while system B doesn't, we're talking apples and oranges and it's irrelevant to 
the diagnosis (and perhaps some systems simply require greater finesse or a 
different protocol).  If one system continually fails on one system and works on 
another, that's what we need to be discussing.  Sorry if I've missed something, 
I'm just getting confused.




 >
 > 4. Are the compilers the same on the iMac vs. AMD cluster?

No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using 
x86_64-redhat-linux 4.1.2 GCC.




Well, I know that for years weird behavior has been attributed to the gcc-4.1.x 
series, including the famous warning on the downloads page:


"WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These 
compilers come with recent Linux distributions like Fedora 5/6 etc."


I don't know if those issues were ever resolved (some error in Gromacs that 
wasn't playing nice with gcc, or vice versa).


I just did a quick yum search and there doesn't seem to be a newer GCC. 
We know you are going to cmake but we have yet to get it implemented on 
our cluster successfully.




The build system is irrelevant.  You still need a reliable C compiler, whether 
using autoconf or cmake.


-Justin

 


Thank you,

TJ Mustard

 


 >
 > -Justin
 >
 > > 
 > >

 > > Now I understand that my iMac works, but it only has 2 cpus and the
 > > cluster has 320. Since we are running our jobs via a Bennet's 
Acceptance

 > > Ratio FEP with 21 lambda windows, using just one 2 cpu machine would
 > > take too long. Especially since we wish to start pseudo high throughput
 > > drug testing.
 > >
 > > 
 > >
 > > 
 > >

 > > In my .mdp files now, the only changes are:
 > >
 > > (the default setting is on the right of the ";")
 > >
 > > 
 > >
 > > 
 > >

 > > define   = ; =
 > >
 > > ; RUN CONTROL PARAMETERS
 > > integrator   = sd; = md
 > > ; Start time and timestep in ps
 > > tinit= 0; = 0
 > > dt   = 0.004; = 0.001
 > > nsteps   = 75   ; = 0 (this one depends on the
 > > window and particular part of our job)
 > >
 > > ; OUTPUT CONTROL OPTIONS
 > > ; Output frequency for coords (x), velocities (v) and forces (f)
 > > nstxout  = 1; = 100 (to save on disk space)
 > > nstvout  = 1; = 100
 > >
 > > 
 > >

 > > ; OPTIONS FOR ELECTROSTATICS AND VDW
 > > ; Method for doing electrostatics
 > > coulombtype  = PME; = Cutoff
 > > rcoulomb-switch  = 0; = 0
 > > rcoulomb = 1  ; = 1
 > > ; Relative dielectric constant for the medium and the reaction field
 > > epsilon_r= 1; = 1
 > > epsilon_rf   = 1; = 1
 > > ; Method for doing Van der Waals
 > > vdw-type = Cut-off; = Cut-off
 > > ; cut-off lengths   
 > > rvdw-switch  = 0; = 0

 > > rvdw = 1  ; = 1
 > > ; Spacing for the PME/PPPM FFT grid
 > > fourierspacing   = 0.12; = 0.12
 > > ; EWALD/PME/PPPM parameters
 > > pme_order= 4; = 4
 > > ewald_rtol   = 1e-05; = 1e-05
 > > ewald_geometry   = 3d; = 3d
 > > epsilon_surface  = 0; = 0
 > > optimize_fft = yes; = no
 > >
 > > 
 > >

 > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
 > > ; Temperature coupling 
 > > tcoupl   = v-rescale; = No

 > > nsttcouple   = -1; = -1
 > > nh-chain-length  = 10; = 10
 > > ; Groups to couple separately
 > > tc-grps  = System; =
 > > ; Time constant (ps) and refe

Re: [gmx-users] (no subject)

[Justin A. Lemkul]

trevor brown wrote:

Dear Justin/Mark,
I would like to have a private course about Gromacs in Holland.
Is there such a facility for this? Who should I talk with?  
 


Can't help you there.  I'm in the U.S.


Or is there a workshop in near future?


Any workshops will surely be announced on the list, but there haven't been any 
Gromacs-specific ones for several years.


-Justin


best wishes
 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at 
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Re: [gmx-users] Two machines, same job, one fails

[TJ Mustard]

  

  
 


  
   On January 25, 2011 at 3:54 PM Mark Abraham  wrote:
  

  


 On 01/26/11, TJ Mustard  wrote: 


  
  

 


  

  
 

 


  On January 25, 2011 at 3:24 PM "Justin A. Lemkul"  wrote:
  
   >
   >
   > TJ Mustard wrote:
   > >
   > >
   > > 
   > >
   > >
   > > On January 25, 2011 at 2:08 PM Mark Abraham  wrote:
   > >
   > >> On 26/01/2011 5:50 AM, TJ Mustard wrote:
   > >>>
   > >>> Hi all,
   > >>>
   > >>> 
   > >>>
   > >>> I am running MD/FEP on a protein-ligand system with gromacs 4.5.3 and
   > >>> FFTW 3.2.2.
   > >>>
   > >>> 
   > >>>
   > >>> My iMac will run the job (over 4000 steps, till I killed it) at 4fs
   > >>> steps. (I am using heavy H)
   > >>>
   > >>> 
   > >>>
   > >>> Once I put this on our groups AMD Cluster the jobs fail even with 2fs
   > >>> steps. (with thousands of lincs errors)
   > >>>
   > >>> 
   > >>>
   > >>> We have recompiled the clusters gromacs 4.5.3 build, with no change.
   > >>> I know the system is the same since I copied the job from the server
   > >>> to my machine, to rerun it.
   > >>>
   > >>> 
   > >>>
   > >>> What is going on? Why can one machine run a job perfectly and the
   > >>> other cannot? I also know there is adequate memory on both machines.
   > >>>
   > >>
   > >> You've posted this before, and I made a number of diagnostic
   > >> suggestions. What did you learn?
   > >>
   > >> Mark
   > >
   > > Mark and all,
   > >
   > > 
   > >
   > > First thank you for all our help. What you suggested last time helped
   > > considerably with our jobs/calculations. I have learned that using the
   > > standard mdp settings allow my heavyh 4fs jobs to run on my iMac (intel)
   > > and have made these my new standard for future jobs. We chose to use the
   > > smaller 0.8nm PME/Cutoff due to others papers/tutorials, but now we
   > > understand why we need these standard settings. Now what I see to be our
   > > problem is that our machines have some sort of variable we cannot
   > > account for. If I am blind to my error, please show me. I just don't
   > > understand why one computer works while the other does not. We have
   > > recompiled gromacs 4.5.3 single precission on our cluster, and still
   > > have this problem.
   > >
   >
   > I know the feeling all too well.  PowerPC jobs crash instantly, on our cluster,
   > despite working beautifully on our lab machines.  There's a bug report about
   > that one, but I haven't heard anything about AMD failures.  It remains a
   > possibility that something beyond your control is going on.  To explore a bit
   > further:
   >
   > 1. Do the systems in question crash immediately (i.e., step zero) or do they run
   > for some time?
   >


Step 0, every time.

 


  > 2. If they give you even a little bit of output, you can analyze which energy
   > terms, etc go haywire with the tips listed here:
   >


All I have seen on these is LINCS Errors and Water molecules unable to be settled.

 

But I will check this out right now, and email if I smell trouble.

 


   

Re: [gmx-users] Two machines, same job, one fails

[TJ Mustard]

  

  
 


  On January 25, 2011 at 3:53 PM "Justin A. Lemkul"  wrote:
  
  >
  >
  > TJ Mustard wrote:
  >
  > 
  >
  > >  > 1. Do the systems in question crash immediately (i.e., step zero) or
  > > do they run
  > >  > for some time?
  > >  >
  > >
  > > Step 0, every time.
  > >
  > > 
  > >
  > >  > 2. If they give you even a little bit of output, you can analyze
  > > which energy
  > >  > terms, etc go haywire with the tips listed here:
  > >  >
  > >
  > > All I have seen on these is LINCS Errors and Water molecules unable to
  > > be settled.
  > >
  > > 
  > >
  > > But I will check this out right now, and email if I smell trouble.
  > >
  > > 
  > >
  > >  >
  > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
  > >  >
  > >  > That would help in tracking down any potential bug or error.
  > >  >
  > >  > 3. Is it just the production runs that are crashing, or everything? 
  > > If EM isn't
  > >  > even working, that smells even buggier.
  > >
  > > Awesome question here, we have seen some weird stuff. Sometimes the
  > > cluster will give us segmentation faults, then it will fail on our
  > > machines or sometimes not on our iMacs. I know weird! If EM starts on
  > > the cluster it will finish. Where we have issues is in positional
  > > restraint (PR) and MD and MD/FEP. It doesn't matter if FEP is on or off
  > > in a MD (although we are using SD for these MD/FEP runs).
  > >
  > > 
  >
  > Does "sometimes" refer to different simulations, or multiple invocations of the
  > same simulation system?  If you're referencing the fact that system A works
  > while system B doesn't, we're talking apples and oranges and it's irrelevant to
  > the diagnosis (and perhaps some systems simply require greater finesse or a
  > different protocol).  If one system continually fails on one system and works on
  > another, that's what we need to be discussing.  Sorry if I've missed something,
  > I'm just getting confused.


 

What trends I see are that some jobs that "segment fault" on the cluster will also fault on our machines. But then when they fail on the cluster, via "segmentation faults", they will work on our machines. Never does a single job "sometimes" fail and sometimes not, it either does or does not, every time. We have just gotten used to rebuilding our system and starting these again. We have also gotten used to doing EM on our machines and transferring this folder to be completed on the cluster. Once there it can finish the PR, MD and FEP.

 


  >
  > >
  > >  >
  > >  > 4. Are the compilers the same on the iMac vs. AMD cluster?
  > >
  > > No I am using x86_64-apple-darwin10 GCC 4.4.4 and the cluster is using
  > > x86_64-redhat-linux 4.1.2 GCC.
  > >
  >
  > Well, I know that for years weird behavior has been attributed to the gcc-4.1.x
  > series, including the famous warning on the downloads page:
  >
  > "WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
  > compilers come with recent Linux distributions like Fedora 5/6 etc."
  >
  > I don't know if those issues were ever resolved (some error in Gromacs that
  > wasn't playing nice with gcc, or vice versa).
  >


 

Yes I am looking into this now. I hope this is our problem and not some hugely time consuming underlying problem with our system. Thank you.

 

Thanks again,

TJ Mustard

 


  > > I just did a quick yum search and there doesn't seem to be a newer GCC.
  > > We know you are going to cmake but we have yet to get it implemented on
  > > our cluster successfully.
  > >
  >
  > The build system is irrelevant.  You still need a reliable C compiler, whether
  > using autoconf or cmake.
  >
  > -Justin
  >
  > > 
  > >
  > > Thank you,
  > >
  > > TJ Mustard
  > >
  > > 
  > >
  > >  >
  > >  > -Justin
  > >  >
  > >  > >
  > >  > >
  > >  > > Now I understand that my iMac works, but it only has 2 cpus and the
  > >  > > cluster has 320. Since we are running our jobs via a Bennet's
  > > Acceptance
  > >  > > Ratio FEP with 21 lambda windows, using just one 2 cpu machine would
  > >  > > take too long. Especially since we wish to start pseudo high throughput
  > >  > > drug testing.
  > >  > >
  > >  > >
  > >  > >
  > >  > >
  > >  > >
  > >  > > In my .mdp files now, the only changes are:
  > >  > >
  > >  > > (the default setting is on the right of the ";")
  > >  > >
  > >  > >
  > >  > >
  > >  > >
  > >  > >
  > >  > > define             

[gmx-users] Fw:Re:gmx-users Digest, Vol 81, Issue 192; PME, Estimate for the relative

[gromacs]

 
 
 

Hi Justin,


.mdp and fourierspacing are at below, can you tell me where is not wrong?



; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off   
rlist= 0.9
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r= 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths  
rvdw-switch  = 0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc  = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling 
Tcoupl   = v-rescale
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Pressure coupling
Pcoupl   = no
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 1
compressibility  = 4.5e-5
ref_p= 1.0
; Random seed for Andersen thermostat
andersen_seed= 815131

; SIMULATED ANNEALING 
; Type of annealing for each temperature group (no/single/periodic)
annealing= no
; Number of time points to use for specifying annealing in each group
annealing_npoints=
; List of times at the annealing points for each group
annealing_time   =
; Temp. at each annealing point, for each group.
annealing_temp   =

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes
gen_temp = 300
gen_seed = 1993










>Message: 4
>Date: Tue, 25 Jan 2011 08:05:44 -0500
>From: "Justin A. Lemkul" 
>Subject: Re: [gmx-users] V-rescale thermostat, PME, Estimate for the
>   relativecomputational load of the PME mesh part: 0.97
>To: Discussion list for GROMACS users 
>Message-ID: <4d3ecaa8.60...@vt.edu>
>Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
>gromacs wrote:
>> HI Friends,
>> 
>> I get the following note,
>> 
>> The Berendsen thermostat does not generate the correct kinetic energy
>>   distribution. You might want to consider using the V-rescale thermostat.
>> 
>> I want to keep the T at 300K, so does it matter to select any thermostat 
>> method?
>> 
>
>The choice of thermostat certainly does matter, otherwise you wouldn't get 
>this 
>note.  Refer to the numerous discussions in the list archive as to why one 
>would 
>or would not (usually) use the Berendsen thermostat, as well as:
>
>http://www.gromacs.org/Documentation/Terminology/Thermostats
>http://www.gromacs.org/Documentation/Terminology/Berendsen
>
>> 
>> Another note when i use PME:
>> 
>> Estimate for the relative computational load of the PME mesh part: 0.97
>> 
>> NOTE 1 [file aminoacids.dat, line 1]:
>>   The optimal PME mesh load for parallel simulations is below 0.5
>>   and for highly parallel simulations between 0.25 and 0.33,
>>   for higher performance, increase the cut-off and the PME grid spacing
>> 
>> So what is the reason? I use type=PME
>> 
>
>Your combination of settings (rcoulomb, fourierspacing, and perhaps a few 
>others) indicate that your simulation is going to spend an inordinate amount 
>of 
>time doing PME calculations, so your performance will suffer.  Seeing your 
>entire .mdp file would be necessary if you want further guidance.
>
>-Justin
>
>> Is my setting proper?
>> 
>> Thanks
>> 
>> 
>
>-- 
>
>
>Justin A. Lemkul
>Ph.D. Cand

Re: [gmx-users] V-rescale thermostat, PME, Estimate for the relative computational load of the PME mesh part: 0.97

[Justin A. Lemkul]

gromacs wrote:
 
 
 


Hi Justin,

.mdp and fourierspacing are at below, can you tell me where is not wrong?




I see nothing "wrong" with the .mdp file, per se, although it does not appear 
complete (no integrator, nsteps, etc).  Perhaps that was your intention, but if 
nsteps is left at default (0), then you shouldn't worry about poor performance :)


The amount of time spent doing PME calculations depends on what is in your 
system.  While your settings seems reasonable in a generic sense, if you have a 
large, highly-charged system, then much of the work will be allocated to PME. 
In that case, you may have to re-think how you balance the real space and 
reciprocal space terms.  This involves possibly increasing (slightly) the values 
of rcoulomb and fourierspacing, if and only if the PME load is prohibitive and 
you are sure you won't incur any unnecessary error.  g_pme_error may help there.


-Justin




; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off   
rlist= 0.9

domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r= 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths  
rvdw-switch  = 0

rvdw = 1.2
; App ly long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   &n bsp;   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc &nbs p;= 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling 
Tcoupl   = v-rescale

; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Pressure coupling
Pcoupl  & nbsp;= no

Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 1
compressibility  = 4.5e-5
ref_p= 1.0
; Random seed for Andersen thermostat
andersen_seed= 815131

; SIMULATED ANNEALING 
; Type of annealing for each temperature group (no/single/periodic)

annealing= no
; Number of time points to use for specify ing annealing in each group
annealing_npoints=
; List of times at the annealing points for each group
annealing_time   =
; Temp. at each annealing point, for each group.
annealing_temp   =

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes
gen_temp = 300
gen_seed = 1993









Message: 4
Date: Tue, 25 Jan 2011 08:05:44 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] V-rescale thermostat, PME, Estimate for the
relativecomputational load of the PME mesh part: 0.97
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4d3ecaa8.60...@vt.edu >
Content-Type: text/plain; charset=UTF-8; format=flowed



gromacs wrote:

HI Friends,

I get the following note,

The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

I want to keep the T at 300K, so does it matter to select any thermostat 
method?




The choice of thermostat certainly does matter, otherwise you wouldn't get this 
note.  Refer to the numerous discussions in the list archive as to why one would 
or would not (usually) use the Berendsen thermostat, as well as:


http://www.gromacs.org/Documentation/Terminology/Thermostats
http://www.gromacs.org/Documenta

[gmx-users] More than one settle type

[Shalabh]

Hi,

I am trying to find the free energy of a water molecule as it adsorbs 
on a surface. My outline is:


1) Run the simulation
2) Analyze the results, find out which water molecule(s) are adsorbed
3) Create different groups for the water adsordbed molecule(s), create 
new .gro file (to identify the adsorbed water with different residue 
name), .mdp file and .tpe file. The remaining water molecules have the 
same previous group name.
4) Use mdrun -rerun to evaluate the energy between the new water 
group(s), the surface and the remaining water.


When I try to implement this, I get an error in step 4 while running 
mdrun -rerun, saying "More than one settle type. Suggestion: change the 
least use settle constraints into 3 normal constraints". The .itp file 
which I created for the new water group is identical to the spc.itp 
file (with the only change as the residue name).


This similar problem was raised earlier as well, which I am not sure 
if it was resolved:

http://lists.gromacs.org/pipermail/gmx-users/2010-January/048058.html

Basically, what I am trying to do is if I have 1000 water molecules in 
my system, can I have 999 of them in one group SOL, and the remaning 1 
water molecule in a different group, say SOL1. The .itp files and 
parameters are identical, apart from the group (residue) name. And I am 
getting the above error. Anyone any ideas?


Thanks in advance!

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Re: [gmx-users] More than one settle type

[Mark Abraham]

On 01/26/11, Shalabh   wrote:
> Hi,
> 
> I am trying to find the free energy of a water molecule as it adsorbs on a 
> surface. My outline is:
> 
> 1) Run the simulation
> 2) Analyze the results, find out which water molecule(s) are adsorbed
> 3) Create different groups for the water adsordbed molecule(s), create new 
> .gro file (to identify the adsorbed water with different residue name), .mdp 
> file and .tpe file. The remaining water molecules have the same previous 
> group name.
> 

You're making life hard for yourself by renaming the residue, which you don't 
need to do. You merely need to divide the solvent into two groups for energy 
evaluation, and you can do that with a suitably constructed index file and 
matching .mdp as grompp input. If you use g_select with a suitable geometric 
criterion for adsorbation, then it can write the index file for you (and there 
are various ways you might visualise the result to check it). All you need to 
do is decide on the criterion, name the groups, modify the .mdp and feed it to 
grompp.


> 
> 4) Use mdrun -rerun to evaluate the energy between the new water group(s), 
> the surface and the remaining water.
> 
> When I try to implement this, I get an error in step 4 while running mdrun 
> -rerun, saying "More than one settle type. Suggestion: change the least use 
> settle constraints into 3 normal constraints". The .itp file which I created 
> for the new water group is identical to the spc.itp file (with the only 
> change as the residue name).
> 
> This similar problem was raised earlier as well, which I am not sure if it 
> was resolved:
> http://lists.gromacs.org/pipermail/gmx-users/2010-January/048058.html
> 
> Basically, what I am trying to do is if I have 1000 water molecules in my 
> system, can I have 999 of them in one group SOL, and the remaning 1 water 
> molecule in a different group, say SOL1. The .itp files and parameters are 
> identical, apart from the group (residue) name. And I am getting the above 
> error. Anyone any ideas?
> 

Groups and molecule blocks in the topology need not relate to each other at 
all. It is simplest to leave your .top file alone and follow the approach I 
suggested above.

Mark
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[gmx-users] QMMM with ORCA

[Xiaohu Li]

Hi, All,
 I'm trying to see if anybody has experience of using the interface of
gromacs and ORCA(since it's free). I know that the following link gave
information on how
http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code
 But.But, the gromacs in the above link is quite old(3.2). I
download the latest 4.5.3 and followed the instructions in the above link
and I was trying to optimize an simple cluster(no pbc) where part of it are
treated using QM. here is the example mdp file
=
title   =  cpeptide
integrator  =  steep   ;integrator includes energy minimization
algorithms
dt  =  0.002; ps !
nsteps  =   1
nstlist =  1
ns_type =  simple
rlist   =  3.0
rcoulomb=  3.0
coulombtype = cut-off
vdwtype = cut-off
rvdw= 3.0
pbc =  no
periodic_molecules  =  no
constraints = none
energygrps  = qm_part mm_part
; QM/MM calculation stuff
QMMM = yes
QMMM-grps = qm_part
QMmethod = rhf
QMbasis = 3-21G
QMMMscheme = oniom
QMcharge = 0
QMmult = 1
;
;   Energy minimizing stuff
;
emtol   =  60   ; minimization thresold (kj/mol.nm-1)1
hartree/bohr= 49614.75241 kj/mol.nm-1  1 kj/mol.nm-1=2.01553e-5 hartree/bohr
emstep  =  0.01  ; minimization step in nm
=
I set up the BASENAME and ORCA_PATH as told in the instruction.
first of all, the normal electronic embedding just simply gave segmentation
fault error right after the it prints information on number of steps of
optimization.

So I switch to ONIOM, this time, at least, orca is called and energy and
gradient are both generated. However, when it comes to read the energy and
gradient, it always crashes when tried to read gradient, this is at *line
346* source code src/mdlib/qm_orca.c

sscanf(buf,"%lf\n", &QMgrad[k][XX]);

a segmentation fault error is printed. If I replace the &QMgrad[k][XX] by an
temporary variable temp
 sscanf(buf,"%lf\n", &temp);
temp gets the correct value and if I use,
QMgrad[k][XX]=temp
and tries to print QMgrad[k][XX], a bus error will be printed.
I did some research online, seems that usually this implies an memory bug in
the code which is the most difficult bug one can ever encounter.
So has anyone successfully used gromacs and orca to do QMMM?
Generally, would anyone recommend using gromacs to do QMMM?

Cheers,
Xiaohu
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[gmx-users] RE: stopping a simulation in between without crashing any trajectories

[bharat gupta]

Hi,

I ran a simulation of 10ns and now it has completed till 5ns ..  I want to
stop it now and retrieve the trajectories without any errors.. Is it
possible to do that ??

-- 
Bharat
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