[gmx-users] Re: eg compilation problem in Mopac gromacs (vidhya sankar)

[Gerrit Groenhof]

You need to compile the mopac library with the modified interface routines and 
link this library. Use the LDFLAGS and LIBS.

Gerrit


> 
> Today's Topics:
> 
>  1. reg compilation problem in Mopac gromacs (vidhya sankar)
>  2. RE: Alanine dipeptide simulations (Dallas Warren)
>  3. Re: Alanine dipeptide simulations (Sai Pooja)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 8 Sep 2010 10:50:49 +0530 (IST)
> From: vidhya sankar 
> Subject: [gmx-users] reg compilation problem in Mopac gromacs
> To: gmx-users@gromacs.org
> Message-ID: <680789.9939...@web95503.mail.in.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear sir, 
> thanks in advance
>  When i type the following command in gromacs directory
> ./configure --with-qmmm-mopac --disable-float
> it configure successfully
> but when i compile by make command i got the following error at the end of my 
> compilation
> 　
> libs/libgmxpreprocess_d.a ../mdlib/.libs/libmd_d.a 
> /root/gromacs-4.0.5/src/gmxlib/.libs/libgmx_d.a ../gmxlib/.libs/libgmx_d.a 
> -lnsl -lfftw3 -lm -lmopac -ltest 
> ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH':
> qm_mopac.c:(.text+0x2a7): undefined reference to `domop_'
> ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac':
> qm_mopac.c:(.text+0x70b): undefined reference to `domop_'
> ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `init_mopac':
> qm_mopac.c:(.text+0x964): undefined reference to `domldt_'
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> make[3]: Leaving directory `/root/gromacs-4.0.5/src/kernel'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/root/gromacs-4.0.5/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/root/gromacs-4.0.5/src'
> make: *** [all-recursive] Error 1
> What should i do to avoid this error? i am expecting your reply
> also when i use ./configure --without-qmmm-mopac --disable-float it compiles 
> successfully
> 
> -- next part --
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> 
> --
> 
> Message: 2
> Date: Wed, 08 Sep 2010 15:27:25 +1000
> From: Dallas Warren 
> Subject: RE: [gmx-users] Alanine dipeptide simulations
> To: Discussion list for GROMACS users 
> Message-ID:
>   <39d19992d8a3804b8c801976acb4596255f...@prk-exch-01.vcp.local>
> Content-Type: text/plain; charset="us-ascii"
> 
> See http://www.gromacs.org/Documentation/Terminology/Pressure for
> further details
> 
> 
> 
> Catch ya,
> 
> Dr. Dallas Warren
> 
> Medicinal Chemistry and Drug Action
> 
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
> 
> +61 3 9909 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble
> a nail. 
> 
> 
> 
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Dallas Warren
> Sent: Wednesday, 8 September 2010 3:21 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] Alanine dipeptide simulations
> 
> 
> 
> What pressure has it reached?
> 
> 
> 
> Probably best graph the pressure versus time plot for the run and show
> that.
> 
> 
> I suspect what you are concerned about is the fact that with pressure
> coupling, the pressure can fluctuation from step to step, very widely,
> 100s atm is not out of the question.
> 
> 
> 
> Catch ya,
> 
> Dr. Dallas Warren
> 
> Medicinal Chemistry and Drug Action
> 
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
> 
> +61 3 9909 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble
> a nail. 
> 
> 
> 
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Sai Pooja
> Sent: Wednesday, 8 September 2010 3:18 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Alanine dipeptide simulations
> 
> 
> 
> Hi,
> 
> I am running an npt simulation on alanine dipeptide in explicit solvent
> using charmm forcefield and tip3p.
> 
> The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
> simulation has been running for 45 ns and has not achieved the target
> average pressure of 1 bar.
> 

[gmx-users] Problem about thread based MPI in Gromacs-4.5.1

[xuji]

Hi all

In Gromacs-4.5 new features, there're
"Running on a multi-core node now uses thread-based parallelization 
to automatically spawn the optimum number of threads in the default build. 
MPI is now only required for parallelization over the network. "

And in Gromacs-4.5 manual, mdurn options has:
"-nt (int 0 Number of threads to start (0 is guess) )"
parameter.

But when use "mdrun -h", the -nt does not exist.
So can the -nt option be used in mdrun? 
And if can, how do I use thread based MPI in mdrun?
Can someone show me an mdrun execution example, please?

Appreciate any help in advance! 

2010-09-08 




Best 
wishes！

Ji Xu
The State Key Laboratory of Multiphase Complex System
Institute of Process Engineering
Chinese Academy of Sciences
Beijing 100190, China
Tel.: +86 10 8262 3713-804 
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Re: [gmx-users] Problem about thread based MPI in Gromacs-4.5.1

[Szilárd Páll]

Hi,

> But when use "mdrun -h", the -nt does not exist.
> So can the -nt option be used in mdrun?

Just checked and If you have threads turned on (!) when building
gromacs then on the help page (mdrun -h) -nt does show up! Otherwise,
it's easy to check if you have thread-enabled build or not: just start
mdrun on a multicore node and see if it uses one thread or all threads
;)

> And if can, how do I use thread based MPI in mdrun?
> Can someone show me an mdrun execution example, please?

As already the information quoted by you underlines, threading is
useful _only_ for multicore parallelism. However, it is not possible
to combine threading and MPI at the moment, if that's what you mean by
"thread based MPI". If you want to parallelize over multiple machines
you'll need to use MPI to parallelize over a single machine's cores as
well.

I hope this helps!

Cheers,
--
Szilárd
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[gmx-users] energygrps

[Poojari, Chetan]

Hi,

I have completed membrane protein simulations. I want to do some free energy 
calculations  but haven't included energygrps in the mdp file.

Please can someone suggest me if theres a way to generate separate energygrps 
for my protein and lipid now as I carried out simulations without having 
energygrps in the mdp file.


cheers,
chetan.



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


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Re: [gmx-users] Alanine dipeptide simulations

[Justin A. Lemkul]

Did you do any form of equilibration prior to the production run?  If so, what? 
 In my experience, an incompletely (or improperly) equilibrated system that is 
passed to the P-R barostat can lead to undesired pressures.  As long as there 
are no systematic influences on your pressure (i.e., trending up or down), then 
you've probably got a stable simulation, especially given the fluctuations.


-Justin

Sai Pooja wrote:

So, what should I aim for when running an NPT simulation?

Pooja

On Wed, Sep 8, 2010 at 1:42 AM, Dallas Warren > wrote:


Is that really that surprising?

 


You have variations of the order of 100s of bar and are looking for
an average that is 1.0

 


What you are observing is nothing out of the ordinary, from my
experience and what others have discussed here on the emailing list.

 


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu 

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to
resemble a nail.

 


*From:* gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org
] *On Behalf Of *Sai Pooja
*Sent:* Wednesday, 8 September 2010 3:38 PM

*To:* Discussion list for GROMACS users
*Subject:* Re: [gmx-users] Alanine dipeptide simulations

 


Hi

Yes, the fluctuations are large but even the average pressure hasn't
converged. Its close 2.5 bar. RMSD ~600 bar.

Pooja

On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren
mailto:dallas.war...@monash.edu>> wrote:

See http://www.gromacs.org/Documentation/Terminology/Pressure for
further details

 


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu 

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to
resemble a nail.

 


*From:* gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org
] *On Behalf Of *Dallas Warren
*Sent:* Wednesday, 8 September 2010 3:21 PM


*To:* Discussion list for GROMACS users

*Subject:* RE: [gmx-users] Alanine dipeptide simulations

 


What pressure has it reached?

 


Probably best graph the pressure versus time plot for the run and
show that.


I suspect what you are concerned about is the fact that with
pressure coupling, the pressure can fluctuation from step to step,
very widely, 100s atm is not out of the question.

 


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu 

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to
resemble a nail.

 


*From:* gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org
] *On Behalf Of *Sai Pooja
*Sent:* Wednesday, 8 September 2010 3:18 PM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] Alanine dipeptide simulations

 


Hi,



I am running an npt simulation on alanine dipeptide in explicit
solvent using charmm forcefield and tip3p.

The pressure is set to 1bar and the barostat is Parrinello-Rahman.
The simulation has been running for 45 ns and has not achieved the
target average pressure of 1 bar.

I don;t understand why is this the case.

My mdp file:

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 50

; OUTPUT CONTROL OPTIONS
nstxout  = 0; No output, except
for last frame (coordinates)
nstvout  = 0; No output, except
for last frame (velocities)
nstfout  = 0; No output, except
for last frame (forces)
nstlog   = 5000; Write every step to
the log
nstenergy= 5000; Write energies
at every step
xtc_grps = Protein SOL
nstxtcout= 5000; Do not write a
compr

Re: [gmx-users] energygrps

[Justin A. Lemkul]

Poojari, Chetan wrote:

Hi,

I have completed membrane protein simulations. I want to do some free energy 
calculations  but haven't included energygrps in the mdp file.

Please can someone suggest me if theres a way to generate separate energygrps 
for my protein and lipid now as I carried out simulations without having 
energygrps in the mdp file.




You can generate a new .tpr file with the proper energygrps and use the mdrun 
-rerun feature.  There are several caveats; check the list archive.


-Justin


cheers,
chetan.



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




--


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] restraining atoms to the plane at the bilayer center: pull code ?

[maria goranovic]

Dear Chris,

Thank you for the code. I did check out pull_pbcatomN, and thank you for the
heads up that it is a global index. I used a central atom in the box for
each of the two groups as pull_pbcatom.

After using the code below with a rate constant of ~ 5500 for about 100 ps,
I realized that the atoms in different leaflets were being pulled in the
same direction.  I wanted certain atoms of either leaflet to be restrained
to the bilayer center. However, the code pulls all the atoms in the same
direction, such that atoms from one leaflet do approach the bilayer center,
but those from the other leaflet tend to get further away from the bilayer
center.  Thus, one actually needs two groups to be pulled, one each for the
atoms in each leaflet. Once this was fixed, the code worked just fine.

Again, thank you.

Maria



On Tue, Sep 7, 2010 at 3:40 PM,  wrote:

> Maria, try this. There actually is a lot of this on the mailing list, so I
> suggest checking it a little deeper for your next querry, or at least
> outlining how you looked and what you found so that it is clear you have
> tried.
>
> Also, read about pull_pbcatomN and think carefully about how you want to
> set that up. It is a *global* index.
>
> ; COM PULLING
> pull = umbrella
> pull_geometry= position
> pull_dim = N N Y
> pull_start   = no
> pull_nstxout = 500
> pull_nstfout = 500
> pull_ngroups = 1
> pull_group0  = <<>>
> pull_pbcatom0= 0
> pull_group1  = <<>>
> pull_pbcatom1= 0
> pull_init1   = 0 0 0.0
> pull_rate1   = 0
> pull_k1  = <<>>
> pull_vec1= 0 0 0
>
> -- original message --
>
>
> The manual does discuss restraining to a plane, but this must be the plane
> in which the atom is already present.
>
> [  position_restraints ]
> ; ai   functfc
> ...
> 3   1   1000   0   0
>
> How about restraining the atom to some other plane? For example, how about
> restraining a phosphate group initially at the lipid-water interface to the
> bilayer center (for whatever fancy reasons) ? Won't this require pulling
> the
> atom to that plane first?
>
> If it can be achieved using the position restraints alone, it is not clear
> to me how to do this?
>
> -Maria
>
>
>
> On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul 
> wrote:
>
>
>>
>> maria goranovic wrote:
>>
>>  I want to restrain certain atoms of my simulation to the plane
>>> perpendicular to the bilayer normal, and at the bilayer center. Can
>>> someone
>>> please provide a quick guide on how to do this? I read the pull-code
>>> options, but restraining to a plane did not seem possible?
>>>
>>>
>>>  You can restrain atoms to a plane using position restraints.  See the
>> manual for an example.
>>
>> -Justin
>>
>>
>>
>>
>>> --
>>> Maria G.
>>> Technical University of Denmark
>>> Copenhagen
>>>
>>>
>>>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] hessian.mtx----> readable format

[Vishal Agarwal]

Thanks Justin

On Tue, Sep 7, 2010 at 5:14 PM, Justin A. Lemkul  wrote:

>
>
> Vishal Agarwal wrote:
>
>> Dear Gromacs Users,
>> Is there a way to convert the hessian.mtx file into a readable format
>> using any of the gromacs utilities?
>>
>
> gmxdump -mtx
> g_nmeig
>
> -Justin
>
>
>  Any help on this would be highly apprecaited..
>> Thanks,
>> Vishal
>>
>>
>>
>>
> --
> 
>
> 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
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>
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[gmx-users] restraining atoms to the plane at the bilayer center: pull code ?

[chris . neale]

Maria,

I highly doubt that you are correct. If you want more help, please  
copy and paste your commands and some relevant output back to the list.


Chris.

--original message --

Message: 4
Date: Wed, 8 Sep 2010 15:07:15 +0200
From: maria goranovic 
Subject: Re: [gmx-users] restraining atoms to the plane at the bilayer
center:pull code ?
To: Discussion list for GROMACS users 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Dear Chris,

Thank you for the code. I did check out pull_pbcatomN, and thank you for the
heads up that it is a global index. I used a central atom in the box for
each of the two groups as pull_pbcatom.

After using the code below with a rate constant of ~ 5500 for about 100 ps,
I realized that the atoms in different leaflets were being pulled in the
same direction.  I wanted certain atoms of either leaflet to be restrained
to the bilayer center. However, the code pulls all the atoms in the same
direction, such that atoms from one leaflet do approach the bilayer center,
but those from the other leaflet tend to get further away from the bilayer
center.  Thus, one actually needs two groups to be pulled, one each for the
atoms in each leaflet. Once this was fixed, the code worked just fine.

Again, thank you.

Maria



On Tue, Sep 7, 2010 at 3:40 PM,  wrote:

[Hide Quoted Text]
Maria, try this. There actually is a lot of this on the mailing list, so I
suggest checking it a little deeper for your next querry, or at least
outlining how you looked and what you found so that it is clear you have
tried.

Also, read about pull_pbcatomN and think carefully about how you want to
set that up. It is a *global* index.

; COM PULLING
pull = umbrella
pull_geometry= position
pull_dim = N N Y
pull_start   = no
pull_nstxout = 500
pull_nstfout = 500
pull_ngroups = 1
pull_group0  = <<>>
pull_pbcatom0= 0
pull_group1  = <<>>
pull_pbcatom1= 0
pull_init1   = 0 0 0.0
pull_rate1   = 0
pull_k1  = <<>>
pull_vec1= 0 0 0

-- original message --


The manual does discuss restraining to a plane, but this must be the plane
in which the atom is already present.

[  position_restraints ]
; ai   functfc
...
3   1   1000   0   0

How about restraining the atom to some other plane? For example, how about
restraining a phosphate group initially at the lipid-water interface to the
bilayer center (for whatever fancy reasons) ? Won't this require pulling
the
atom to that plane first?

If it can be achieved using the position restraints alone, it is not clear
to me how to do this?

-Maria



On Tue, Sep 7, 2010 at 12:53 PM, Justin A. Lemkul 
wrote:

maria goranovic wrote:

  I want to restrain certain atoms of my simulation to the plane
perpendicular to the bilayer normal, and at the bilayer center. Can
someone
please provide a quick guide on how to do this? I read the pull-code
options, but restraining to a plane did not seem possible?


  You can restrain atoms to a plane using position restraints.  See the
manual for an example.
-Justin
--
Maria G.
Technical University of Denmark
Copenhagen

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[gmx-users] How to select atoms dynamically

[zhongjin]

Hi,  I want to analyze the local density of water in CNT,but the water in CNT 
are not static,in one frame, it is in the CNT,but in another frame, it is may 
not ,how to select the waters in CNT DYNAMICALLY?Zhongjin He


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Re: [gmx-users] How to select atoms dynamically

[Justin A. Lemkul]

zhongjin wrote:

Hi,
  I want to analyze the local density of water in CNT,but the water in 
CNT are not static,in one frame, it is in the CNT,but in another frame, 
it is may not ,how to select the waters in CNT DYNAMICALLY?


There is a new tool in the 4.5 release called g_select.  It may suit your needs.

-Justin


Zhongjin He


 



--


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
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Re: [gmx-users] How to select atoms dynamically

[Elton Carvalho]

On Wed, Sep 8, 2010 at 11:23 AM, zhongjin  wrote:
>
> Hi,
>   I want to analyze the local density of water in CNT,but the water in CNT 
> are not static,in one frame, it is in the CNT,but in another frame, it is may 
> not ,how to select the waters in CNT DYNAMICALLY?
> Zhongjin He

Hello, zhongjin.

May I contact you off-list with some questions about CNT in GROMACS?

--
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Instituto de Física
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[gmx-users] dihedrals potential as a expansion of cosine funtions

[Javier Cerezo]

Hi all.

I am a bit confused about how GROMACS handles multiply defined 
interactions in the top file. Concretely, I see from the lipid 
parameters (POPC) from Kukol (JCTC, 5:615, updated in 
http://lists.gromacs.org/pipermail/gmx-users/2010-May/050647.html ) that 
when defining several times an interaction it is sum up. However, it was 
also stated by Mark Abraham that just the last definition in the top 
file is taken into account 
(http://lists.gromacs.org/pipermail/gmx-users/2007-January/025316.html):

Quote:

<<
For purposes of GROMACS, a bonded function is defined by the function type
(an integer) and the set of atoms to which it applies. See table 5.4.
There may only be one instance of a given function type for a given set of
atoms. grompp will take the last such function that it finds. Thus you
cannot have multiple periodic dihedral functions on the same four atoms,
even if their multiplicity varies.





Could anyone help me with that? How will GROMACS-4 interpret multiply 
defined interaction?


Many thanks!

Javier

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Javier CEREZO BASTIDA
Estudiante de Doctorado
-
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434

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[gmx-users] g_rdf between bonded and nonbonded groups

[Emily Curtis]

I would like to calculate the inter- and intra-molecular radial distribution
functions separately.  I have read through g_rdf -h many times and I have a
few questions:

1.  I think that I may have to modify a trp file (and not use it for the
simulations) by setting the nrexcl to the number of bonds I would like the
calculation to exclude.  I cannot figure out where in the tpr file I should
add the nrexcl term.  I have tried to sort through the manual to figure out
how to make this modification but I cannot figure it out.  Does anyone have
any suggestions?

2.  In D.56 g_rdf of the Gromacs manual it says that the option -surf can be
used along with -rdf to only calculate the rdf of a molecule with its
closest neighbor in a set.  Can this option be used for calculating the
intramolecular radial distribution function or am I completely
misinterpreting the manual?  If it can be used how is this done?  I tried to
use it but I get the error message:  Invalid command line argument:
-surf

Thank you in advance for any help.

Emily
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Re: [gmx-users] g_rdf between bonded and nonbonded groups

[Justin A. Lemkul]

Emily Curtis wrote:



I would like to calculate the inter- and intra-molecular radial 
distribution functions separately.  I have read through g_rdf -h many 
times and I have a few questions:


1.  I think that I may have to modify a trp file (and not use it for the 
simulations) by setting the nrexcl to the number of bonds I would like 
the calculation to exclude.  I cannot figure out where in the tpr file I 
should add the nrexcl term.  I have tried to sort through the manual to 
figure out how to make this modification but I cannot figure it out. 
 Does anyone have any suggestions?




You set nrexcl in the topology, not directly in the .tpr file.

2.  In D.56 g_rdf of the Gromacs manual it says that the option -surf 
can be used along with -rdf to only calculate the rdf of a molecule with 
its closest neighbor in a set.  Can this option be used for calculating 
the intramolecular radial distribution function or am I completely 
misinterpreting the manual?  If it can be used how is this done?  I 
tried to use it but I get the error message:  Invalid command line argument:

-surf


What is your exact command line?  Which version of Gromacs are you using?  In 
the latest version I cannot reproduce this error.


-Justin



Thank you in advance for any help.

Emily



--


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] dihedrals potential as a expansion of cosine funtions

[Mark Abraham]

- Original Message -
From: Javier Cerezo 
Date: Thursday, September 9, 2010 3:17
Subject: [gmx-users] dihedrals potential as a expansion of cosine funtions
To: gmx-users@gromacs.org

> Hi all.
> 
> I am a bit confused about how GROMACS handles multiply defined 
> interactions in the top file. Concretely, I see from the lipid 
> parameters (POPC) from Kukol (JCTC, 5:615, updated in 
> http://lists.gromacs.org/pipermail/gmx-users/2010-
> May/050647.html ) that when defining several times an 
> interaction it is sum up. However, it was also stated by Mark 
> Abraham that just the last definition in the top file is taken 
> into account (http://lists.gromacs.org/pipermail/gmx-users/2007-
> January/025316.html):Quote:
> 
> <<
> For purposes of GROMACS, a bonded function is defined by the 
> function type
> (an integer) and the set of atoms to which it applies. See table 5.4.
> There may only be one instance of a given function type for a 
> given set of
> atoms. grompp will take the last such function that it finds. 
> Thus you
> cannot have multiple periodic dihedral functions on the same 
> four atoms,
> even if their multiplicity varies.
> >>
> 
> 
> Could anyone help me with that? How will GROMACS-4 interpret 
> multiply defined interaction?

GROMACS behaves differently when looking up parameters for a dihedral function 
from the [dihedraltypes] than when assembling dihedral functions whose 
parameters are already supplied in [dihedrals]. (Some time since 2007 you will 
find a post from Berk that corrects me on this point :-)) The GROMOS 
forcefields use the latter method via the gb_xx cpp macros. These add. You can 
verify this simply by adding a duplicate of a single [dihedral] and observing 
that the Step 0 energy will change.

Normal [dihedraltypes] of the same "kind" do not add, except for type 9 
(introduced in GROMACS 4.5) which caters to aspects of CHARMM and AMBER force 
fields.

Now that I think about it, perhaps a sentence is needed in the manual treating 
this case. Will check there.

Mark

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Re: [gmx-users] g_rdf between bonded and nonbonded groups

[Emily Curtis]

Hi Justin,

Thank you for your help.  I will edit the topology file.  I am running
GROMACS 4.0.7.  I can download the latest version.  The command line I was
using was:

g_rdf -n index -rdf res_com -s full -surf  -o rdf08SEPT10.xvg

Emily


On Wed, Sep 8, 2010 at 5:31 PM, Emily Curtis wrote:

> Hi Justin,
>
> Thank you for your help.  I will edit the topology file.  I am running
> GROMACS 4.0.7.  I can download the latest version.  The command line I was
> using was:
>
> g_rdf -n index -rdf res_com -s full -surf  -o rdf08SEPT10.xvg
>
> Emily
>
> On Wed, Sep 8, 2010 at 4:05 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Emily Curtis wrote:
>>
>>>
>>>
>>> I would like to calculate the inter- and intra-molecular radial
>>> distribution functions separately.  I have read through g_rdf -h many times
>>> and I have a few questions:
>>>
>>> 1.  I think that I may have to modify a trp file (and not use it for the
>>> simulations) by setting the nrexcl to the number of bonds I would like the
>>> calculation to exclude.  I cannot figure out where in the tpr file I should
>>> add the nrexcl term.  I have tried to sort through the manual to figure out
>>> how to make this modification but I cannot figure it out.  Does anyone have
>>> any suggestions?
>>>
>>>
>> You set nrexcl in the topology, not directly in the .tpr file.
>>
>>
>>  2.  In D.56 g_rdf of the Gromacs manual it says that the option -surf can
>>> be used along with -rdf to only calculate the rdf of a molecule with its
>>> closest neighbor in a set.  Can this option be used for calculating the
>>> intramolecular radial distribution function or am I completely
>>> misinterpreting the manual?  If it can be used how is this done?  I tried to
>>> use it but I get the error message:  Invalid command line argument:
>>> -surf
>>>
>>
>> What is your exact command line?  Which version of Gromacs are you using?
>>  In the latest version I cannot reproduce this error.
>>
>> -Justin
>>
>>
>>
>>> Thank you in advance for any help.
>>>
>>> Emily
>>>
>>>
>> --
>> 
>>
>> 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
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>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] g_rdf between bonded and nonbonded groups

[Justin A. Lemkul]

Emily Curtis wrote:

Hi Justin,

Thank you for your help.  I will edit the topology file.  I am running 
GROMACS 4.0.7.  I can download the latest version.  The command line I 


There's your problem.  The -surf option only appears as of version 4.5.


was using was:

g_rdf -n index -rdf res_com -s full -surf  -o rdf08SEPT10.xvg



As an aside (which you will surely discover by reading g_rdf -h), the -surf
option requires a string after it; it is not a simple boolean.

-Justin


Emily

On Wed, Sep 8, 2010 at 4:05 PM, Justin A. Lemkul > wrote:




Emily Curtis wrote:



I would like to calculate the inter- and intra-molecular radial
distribution functions separately.  I have read through g_rdf -h
many times and I have a few questions:

1.  I think that I may have to modify a trp file (and not use it
for the simulations) by setting the nrexcl to the number of
bonds I would like the calculation to exclude.  I cannot figure
out where in the tpr file I should add the nrexcl term.  I have
tried to sort through the manual to figure out how to make this
modification but I cannot figure it out.  Does anyone have any
suggestions?


You set nrexcl in the topology, not directly in the .tpr file.


2.  In D.56 g_rdf of the Gromacs manual it says that the option
-surf can be used along with -rdf to only calculate the rdf of a
molecule with its closest neighbor in a set.  Can this option be
used for calculating the intramolecular radial distribution
function or am I completely misinterpreting the manual?  If it
can be used how is this done?  I tried to use it but I get the
error message:  Invalid command line argument:
-surf


What is your exact command line?  Which version of Gromacs are you
using?  In the latest version I cannot reproduce this error.

-Justin



Thank you in advance for any help.

Emily


-- 



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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--


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] Overflow problem with test-particle insertion

[Kevin Daly]

Hello Gromacs users,

I sent a message to the list in June describing what appeared to be a float
overflow issue with the energy calculation for test-particle insertions:
http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html.

I have recently tried the test-particle insertion mode in Gromacs-4.5.1, and
it seems the problem is still there. Does anyone know how to work around or
fix this problem without using tabulated potentials?

-Kevin
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[gmx-users] Re: multiplication of lambda constant with LJ potential affecting only solvent.

[Navjeet Ahalawat]

Hi all

I want to change LJ potential for water only by multiplying a factor lambda.
Can anybody help me that it affect only water not protein.

Thanks in advance.

-- 
Navjeet Ahalawat
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