RE: [gmx-users] Re: [ atomtypes ] are not case sensitive?

[Berk Hess]

Yes. I changed this, since it is required for Amber support with proper atom 
type names.

But I seem to have forgotten to add it to the 4.5 release notes.



Berk

From: awil...@ebi.ac.uk
Date: Thu, 6 Jan 2011 10:23:25 +
To: gmx-users@gromacs.org
CC: 
Subject: [gmx-users] Re: [ atomtypes ] are not case sensitive?

Dear GMX list,
It's more the 2 years ago and now with my gmx.top file containing:
[ atomtypes ];name   bond_type mass charge   ptype   sigma 
epsilon   Amb

 CA   CA  0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860 caca   0.  0.  A   3.39967e-01  3.59824e-01
And using GMX 4.5 and I don't see this complain anymore:


WARNING 1 [file system_GMX.top, line 43]:  Overriding atomtype CA
Should I assume that gromacs finally made its atomtypes case sensitive? Only 
version 4.5 and above?


Many thanks,
Alan 

On 21 August 2008 09:07, Alan  wrote:


Well, I didn't developed Amber FF neither GAFF and although only Amber FF is 
ported to GMX, one of the greatest appealing of Amber is its antechamber and 
GAFF for generating topology for non usual compounds.




Looking at the way GAFF was developed (remember G is for generalised) is seemed 
a natural step to me to use the same name for atom types but using a different 
cases.
So have said that, I did a look at my converted topology file by amb2gmx/acpypi 
and found that, although for vdw parameters they seem the same, this doesn't 
hold for bonds for example. I have this in my GMX top file:




[ bonds ]...96 97   11.0800e-013.0711e+05 ;CZ2 - HZ2 (AT CA - 
HA) Protein
...3154   3194   11.0870e-012.8811e+05 ;C76 - H76 (AT ca - ha) 
Ligand





Anyway, after all this discussion, I realized (correct if I am wrong please) 
that as long as the vdw parameters are the same, anything else is NOT affected 
because even for the example of bonds above atom types change nothing since 
parameters are explicit.




Then, I decided to compare gaff.dat and parm99.dat (topology parameters files 
for Amber package) for vdw. I did found 2 atom types with same name (diff case 
though) and diff parameters:



parm99.dat   HP  1.1000  0.0157 Veenstra et al 
JCC,8,(1992),963   Na  1.8680  0.00277Na+ Aqvist JPC 
1990,94,8021. (adapted)



gaff.dat   hp  0.6000  0.0157 same to hs (be careful !)
na  1.8240  0.1700 OPLS
Observe by the comments (4th column) that although they have the same name (but 
diff by case) they are completely unrelated, hence the diff values for r0 and 
epsilon.



So, in the end, at least for example gaff.dat x parm99.dat (note that Amber has 
several others parm*.dat and glycam*.dat), I do have a conflicting case issue 
that would affect my topology in GMX format if using amb2gmx/acpypi tool for 
conversion.



Pondering a bit more, I came to the conclusion that at least for acpypi (which 
I am developing), I can make it aware of this conflicting atom type naming 
issue and rename it when converting from Amber to GMX.



About changing something in GMX? Frankly I don't know, but I hope that this 
thread can be of some use for someone else who stumbles in this problem.
Cheers and many thanks for attention dear Berk.



Alan

From: Berk Hess 





Subject: RE: [gmx-users] RE: [ atomtypes ] are not case sensitive?
Hi,



I don't know if any thinking went into the (non) case specifity of atom types.

Nearly all string comparisons in Gromacs are not case specific.

For things like atom names this makes sense.



We could change the atom type comparisons to case specific.

I think that all force field files supplied with Gromacs have consistent cases.

But some users might have made force fields where this would cause problems.



I think it is bad practice to distinguish atom types just by case,

this makes things quite error prone.

But allowing this probably does not mean that many people would do this.



Another option would be to add an option to grompp.



Berk.





Date: Tue, 19 Aug 2008 12:03:57 +0100

From: alanwil...@gmail.com

To: gmx-users@gromacs.org

Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive?



Dear Berk,

Thanks for your attention.

I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am just 
learning since I am trying to test an application that is related to amb2gmx 
and ffamber (acpypi).



So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field (GAFF) 
uses all the atom types (AT) usually defined for Amber FF and several more AT 
but in lower case. I cannot assure 100% but I believe that for all common AT 
(being upper or lower), they share the same parameters including when found in 
bonds, angles etc. parameters.







If so, then, it's not a problem if GMX is not sensitive about AT lower or upper 
case, because in the end they are the same. But, as I said before, I am not 
100% sure about it. 

[gmx-users] Re: methanol simulation error

[mustafa bilsel]

Hi Mark,
her is my topology,

best wishes
mustafa
;
;File 'topol.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Fri Jan  7 00:19:16 2011
;
;This is a standalone topology file
;
;It was generated using program:
;pdb2gmx - VERSION 4.5.1
;
;Command line was:
;pdb2gmx -f vpgvg10.pdb -ignh
;
;Force field was read from the standard Gromacs share directory.
;

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

[ moleculetype ]
; Namenrexcl
Protein 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   1 VAL rtp VAL  q +1.0
 1 NL  1VAL  N  1  0.12914.0067   ; qtot
0.129
 2  H  1VAL H1  1  0.248  1.008   ; qtot
0.377
 3  H  1VAL H2  1  0.248  1.008   ; qtot
0.625
 4  H  1VAL H3  1  0.248  1.008   ; qtot
0.873
 5CH1  1VAL CA  2  0.127 13.019   ; qtot
1
 6CH1  1VAL CB  2  0 13.019   ; qtot
1
 7CH3  1VALCG1  2  0 15.035   ; qtot
1
 8CH3  1VALCG2  2  0 15.035   ; qtot
1
 9  C  1VAL  C  3   0.38 12.011   ; qtot
1.38
10  O  1VAL  O  3  -0.3815.9994   ; qtot
1
; residue   2 PRO rtp PRO  q  0.0
11  N  2PRO  N  4  014.0067   ; qtot
1
12CH1  2PRO CA  5  0 13.019   ; qtot
1
13CH2  2PRO CB  5  0 14.027   ; qtot
1
14CH2  2PRO CG  6  0 14.027   ; qtot
1
15CH2  2PRO CD  6  0 14.027   ; qtot
1
16  C  2PRO  C  7   0.38 12.011   ; qtot
1.38
17  O  2PRO  O  7  -0.3815.9994   ; qtot
1
; residue   3 GLY rtp GLY  q  0.0
18  N  3GLY  N  8  -0.2814.0067   ; qtot
0.72
19  H  3GLY  H  8   0.28  1.008   ; qtot
1
20CH2  3GLY CA  9  0 14.027   ; qtot
1
21  C  3GLY  C 10   0.38 12.011   ; qtot
1.38
22  O  3GLY  O 10  -0.3815.9994   ; qtot
1
; residue   4 VAL rtp VAL  q  0.0
23  N  4VAL  N 11  -0.2814.0067   ; qtot
0.72
24  H  4VAL  H 11   0.28  1.008   ; qtot
1
25CH1  4VAL CA 12  0 13.019   ; qtot
1
26CH1  4VAL CB 12  0 13.019   ; qtot
1
27CH3  4VALCG1 12  0 15.035   ; qtot
1
28CH3  4VALCG2 12  0 15.035   ; qtot
1
29  C  4VAL  C 13   0.38 12.011   ; qtot
1.38
30  O  4VAL  O 13  -0.3815.9994   ; qtot
1
; residue   5 GLY rtp GLY  q  0.0
31  N  5GLY  N 14  -0.2814.0067   ; qtot
0.72
32  H  5GLY  H 14   0.28  1.008   ; qtot
1
33CH2  5GLY CA 15  0 14.027   ; qtot
1
34  C  5GLY  C 16   0.38 12.011   ; qtot
1.38
35  O  5GLY  O 16  -0.3815.9994   ; qtot
1
; residue   6 VAL rtp VAL  q  0.0
36  N  6VAL  N 17  -0.2814.0067   ; qtot
0.72
37  H  6VAL  H 17   0.28  1.008   ; qtot
1
38CH1  6VAL CA 18  0 13.019   ; qtot
1
39CH1  6VAL CB 18  0 13.019   ; qtot
1
40CH3  6VALCG1 18  0 15.035   ; qtot
1
41CH3  6VALCG2 18  0 15.035   ; qtot
1
42  C  6VAL  C 19   0.38 12.011   ; qtot
1.38
43  O  6VAL  O 19  -0.3815.9994   ; qtot
1
; residue   7 PRO rtp PRO  q  0.0
44  N  7PRO  N 20  014.0067   ; qtot
1
45CH1  7PRO CA 21  0 13.019   ; qtot
1
46CH2  7PRO CB 21  0 14.027   ; qtot
1
47CH2  7PRO CG 22  0 14.027   ; qtot
1
48CH2  7PRO CD 22  0 14.027   ; qtot
1
49  C  7PRO  C 23   0.38 12.011   ; qtot
1.38
50  O  7PRO  O 23  -0.3815.9994   ; qtot
1
; residue   8 GLY rtp GLY  q  0.0
51  N  8GLY  N 24  -0.2814.0

[gmx-users] number of index elements not multiple of 3, these can not be angle triplet

[Carla Jamous]

Hi Everyone,

Please I'm trying to calculate one dihedral angle as a function of time
during my simulation.
For this, I used g_angle. In the manual (version 4.0.3) it says: the
indexfile should contain atom-triplets or atom-quadruplets for dihedrals.

I put an atom-quadruplet in my index file, but when I run
g_angle -f .xtc -n .ndx -od .xvg

and I select the group of atom-quadruplets, gromacs crashes and shows this
error message:
number of index elements not multiple of 3, these can not be angle triplets

So actually g_angle only calculates angles not dihedrals?

Thanks

Carla
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Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

[Mark Abraham]

On 7/01/2011 9:16 PM, Carla Jamous wrote:

Hi Everyone,

Please I'm trying to calculate one dihedral angle as a function of 
time during my simulation.
For this, I used g_angle. In the manual (version 4.0.3) it says: the 
indexfile should contain atom-triplets or atom-quadruplets for dihedrals.


I put an atom-quadruplet in my index file, but when I run
g_angle -f .xtc -n .ndx -od .xvg

and I select the group of atom-quadruplets, gromacs crashes and shows 
this error message:
number of index elements not multiple of 3, these can not be angle 
triplets


So actually g_angle only calculates angles not dihedrals?


See -type in g_angle -h.

Mark
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Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

[Amit Choubey]

try the -type option with dihedral

amit

On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous  wrote:

> Hi Everyone,
>
> Please I'm trying to calculate one dihedral angle as a function of time
> during my simulation.
> For this, I used g_angle. In the manual (version 4.0.3) it says: the
> indexfile should contain atom-triplets or atom-quadruplets for dihedrals.
>
> I put an atom-quadruplet in my index file, but when I run
> g_angle -f .xtc -n .ndx -od .xvg
>
> and I select the group of atom-quadruplets, gromacs crashes and shows this
> error message:
> number of index elements not multiple of 3, these can not be angle triplets
>
> So actually g_angle only calculates angles not dihedrals?
>
> Thanks
>
> Carla
>
>
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Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

[Carla Jamous]

Thank you,

It worked, one last question. Something is not very clear to me:

-ov: plots the average angle of a group of angles as a function of time!!
What does it mean?

Because I'm getting positive and negative values in the same plot. Are these
values the values of my dihedral angle as a function of time?

Thanks again,
Carla

On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey  wrote:

> try the -type option with dihedral
>
> amit
>
> On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous wrote:
>
>> Hi Everyone,
>>
>> Please I'm trying to calculate one dihedral angle as a function of time
>> during my simulation.
>> For this, I used g_angle. In the manual (version 4.0.3) it says: the
>> indexfile should contain atom-triplets or atom-quadruplets for dihedrals.
>>
>> I put an atom-quadruplet in my index file, but when I run
>> g_angle -f .xtc -n .ndx -od .xvg
>>
>> and I select the group of atom-quadruplets, gromacs crashes and shows this
>> error message:
>> number of index elements not multiple of 3, these can not be angle
>> triplets
>>
>> So actually g_angle only calculates angles not dihedrals?
>>
>> Thanks
>>
>> Carla
>>
>>
>> --
>>
>> 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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>>
>
>
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Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

[Amit Choubey]

Yes -ov does give you average angle as a function of time. I am not sure if
this answers your question though.

amit

On Fri, Jan 7, 2011 at 2:40 AM, Carla Jamous  wrote:

> Thank you,
>
> It worked, one last question. Something is not very clear to me:
>
> -ov: plots the average angle of a group of angles as a function of time!!
> What does it mean?
>
> Because I'm getting positive and negative values in the same plot. Are
> these values the values of my dihedral angle as a function of time?
>
> Thanks again,
> Carla
>
>
> On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey  wrote:
>
>> try the -type option with dihedral
>>
>> amit
>>
>> On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous wrote:
>>
>>> Hi Everyone,
>>>
>>> Please I'm trying to calculate one dihedral angle as a function of time
>>> during my simulation.
>>> For this, I used g_angle. In the manual (version 4.0.3) it says: the
>>> indexfile should contain atom-triplets or atom-quadruplets for dihedrals.
>>>
>>> I put an atom-quadruplet in my index file, but when I run
>>> g_angle -f .xtc -n .ndx -od .xvg
>>>
>>> and I select the group of atom-quadruplets, gromacs crashes and shows
>>> this error message:
>>> number of index elements not multiple of 3, these can not be angle
>>> triplets
>>>
>>> So actually g_angle only calculates angles not dihedrals?
>>>
>>> Thanks
>>>
>>> Carla
>>>
>>>
>>> --
>>>
>>> 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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>>>
>>
>>
>> --
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>
>
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Re: [gmx-users] trjconv with multiple chains

[Amit Choubey]

Make your box bigger?

2011/1/6 yuanyuan wang 

> dear all,
>  I am doing a simulation that have many chains in a box , and I can
> find a center for them after serval tries.
>  I use almost every option of trjconv,-pbc
> mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box,
> and -boxcenter, -fit ..
>  still some chain cannot convert into box. them jump from one box
> to another ,
>  is there any ways that they not jump to another box?
>  thanks a lot.
>
>
> yuanyuan
>
>
>
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Re: [gmx-users] Re: methanol simulation error

[Justin A. Lemkul]

mustafa bilsel wrote:




; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

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



This topology defines the [moleculetype] name as "Methanol," which is the name 
that needs to be used in the [molecules] directive below.  But then, too, you're 
not using the same residue name either (MTH instead of MeOH), so it is still not 
possible to say what's going wrong.


-Justin


[ system ]
; Name
Protein in methanol

[ molecules ]
; Compound#mols
Protein 1
MTH   660



--


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] number of index elements not multiple of 3, these can not be angle triplet

[Justin A. Lemkul]

Carla Jamous wrote:

Thank you,

It worked, one last question. Something is not very clear to me:

-ov: plots the average angle of a group of angles as a function of 
time!! What does it mean?


Because I'm getting positive and negative values in the same plot. Are 
these values the values of my dihedral angle as a function of time?




The -ov option gives the average angle of all angles contained in the index 
group over time.  If your selected group contains only one angle, then the 
average at any given time is equal to the instantaneous value at that time.


-Justin


Thanks again,
Carla

On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey > wrote:


try the -type option with dihedral

amit

On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous mailto:carlajam...@gmail.com>> wrote:

Hi Everyone,

Please I'm trying to calculate one dihedral angle as a function
of time during my simulation.
For this, I used g_angle. In the manual (version 4.0.3) it says:
the indexfile should contain atom-triplets or atom-quadruplets
for dihedrals.

I put an atom-quadruplet in my index file, but when I run
g_angle -f .xtc -n .ndx -od .xvg

and I select the group of atom-quadruplets, gromacs crashes and
shows this error message:
number of index elements not multiple of 3, these can not be
angle triplets

So actually g_angle only calculates angles not dihedrals?

Thanks

Carla


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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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Re: [gmx-users] trjconv with multiple chains

[Justin A. Lemkul]

Amit Choubey wrote:

Make your box bigger?



Box size is unrelated to trjconv.  Periodicity effects will still apply - things 
will diffuse no matter how large you try to make the box.


-Justin


2011/1/6 yuanyuan wang mailto:yilin3...@126.com>>

dear all,
 I am doing a simulation that have many chains in a box ,
and I can find a center for them after serval tries.
 I use almost every option of trjconv,-pbc
mol,atom,res,whole,nojump , -ur compact, -center , -box to got
bigger box, and -boxcenter, -fit ..
 still some chain cannot convert into box. them jump from
one box to another ,
 is there any ways that they not jump to another box?
 thanks a lot.
 
 
yuanyuan




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Department of Biochemistry
Virginia Tech
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[gmx-users] To make continuous trj in REMD

[Qin Qiao]

Dear all,

I came across a problem when I want to make the REMD trajectories
continuous.

What I did:

1. 'demux.pl REMD_0.log'  --to get the 'replica_index.xvg'
2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg'

It seems smooth. But when I check the rmsd of the output 0_resort.xtc, I
found it's still discontinuous.. with big jumps about 0.5nm..! Could you
help me to figure out what's wrong? Thanks a lot.

Best,

Qin
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Re: [gmx-users] To make continuous trj in REMD

[Justin A. Lemkul]

Qin Qiao wrote:

Dear all,

I came across a problem when I want to make the REMD trajectories 
continuous.


What I did:

1. 'demux.pl  REMD_0.log'  --to get the 
'replica_index.xvg'

2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg'

It seems smooth. But when I check the rmsd of the output 0_resort.xtc, I 
found it's still discontinuous.. with big jumps about 0.5nm..! Could you 
help me to figure out what's wrong? Thanks a lot.




Have you properly accounted for periodicity effects?

-Justin


Best,

Qin



--


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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[gmx-users] inconsistent energies

[Vlad Isaev]

Hi,

I want to calculate the energy of a peptide. No minimization, or md, just
the energy at 0 K. I use this input:

integrator   = steep
nsteps   = 0
nstenergy= 1
nstlist  = 0
ns_type  = simple
pbc  = no
rlist= 0
rcoulomb = 0
rvdw = 0


I get:

Potential Energy  = -1.1744482e+02

Changing steep to cg changes the potential energy even though nsteps=0:

Potential Energy  = -1.2410449e+02

The corresponding energy from AMBER10 is : -1.20172848e+02 (conversion
factor 4.184).

Any ideas why these are so different?

Many thanks,
Vlad
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Re: [gmx-users] To make continuous trj in REMD

[Qin Qiao]

2011/1/7 Justin A. Lemkul 

>
>
> Qin Qiao wrote:
>
>> Dear all,
>>
>> I came across a problem when I want to make the REMD trajectories
>> continuous.
>>
>> What I did:
>>
>> 1. 'demux.pl  REMD_0.log'  --to get the
>> 'replica_index.xvg'
>>
>> 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg'
>>
>> It seems smooth. But when I check the rmsd of the output 0_resort.xtc, I
>> found it's still discontinuous.. with big jumps about 0.5nm..! Could you
>> help me to figure out what's wrong? Thanks a lot.
>>
>>
> Have you properly accounted for periodicity effects?
>
> -Justin
>

It's the same after I remove periodicity by trjconv -pbc mol -ur compact ...


>  Best,
>>
>> Qin
>>
>> --
> 
>
> 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] To make continuous trj in REMD

[Justin A. Lemkul]

Qin Qiao wrote:



2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>>



Qin Qiao wrote:

Dear all,

I came across a problem when I want to make the REMD
trajectories continuous.

What I did:

1. 'demux.pl   REMD_0.log'
 --to get the 'replica_index.xvg'


2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux
../replica_index.xvg'

It seems smooth. But when I check the rmsd of the output
0_resort.xtc, I found it's still discontinuous.. with big jumps
about 0.5nm..! Could you help me to figure out what's wrong?
Thanks a lot.


Have you properly accounted for periodicity effects?

-Justin


It's the same after I remove periodicity by trjconv -pbc mol -ur compact ...
 


One iteration of trjconv is not necessarily enough to produce a properly imaged 
trajectory.  What is going on in the trajectory when these spikes are occurring?


-Justin



Best,

Qin

-- 



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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Re: [gmx-users] To make continuous trj in REMD

[Qin Qiao]

2011/1/7 Justin A. Lemkul 

>
>
> Qin Qiao wrote:
>
>>
>>
>> 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>Qin Qiao wrote:
>>
>>Dear all,
>>
>>I came across a problem when I want to make the REMD
>>trajectories continuous.
>>
>>What I did:
>>
>>1. 'demux.pl   REMD_0.log'
>>   --to get the 'replica_index.xvg'
>>
>>
>>2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux
>>../replica_index.xvg'
>>
>>It seems smooth. But when I check the rmsd of the output
>>0_resort.xtc, I found it's still discontinuous.. with big jumps
>>about 0.5nm..! Could you help me to figure out what's wrong?
>>Thanks a lot.
>>
>>
>>Have you properly accounted for periodicity effects?
>>
>>-Justin
>>
>>
>> It's the same after I remove periodicity by trjconv -pbc mol -ur compact
>> ...
>>
>>
>
> One iteration of trjconv is not necessarily enough to produce a properly
> imaged trajectory.  What is going on in the trajectory when these spikes are
> occurring?
>
> -Justin
>
> In VMD, it just seems to change to a different conformation...

   Best,
>>
>>Qin
>>
>>-- 
>>
>>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
>>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
>>
>>
>>
> --
> 
>
> 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: Re: methanol simulation error

[mustafa bilsel]

Daer Justin,
I changed the last line as
MTH 660

I got the same error,
Atomtype CMET not found

Do you mean this?

best wishes
mustafa




Message: 1
Date: Fri, 07 Jan 2011 07:04:05 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Re: methanol simulation error
To: Discussion list for GROMACS users 
Message-ID: <4d270135.5000...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



mustafa bilsel wrote:



> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "gromos43a1.ff/methanol.itp"
>

This topology defines the [moleculetype] name as "Methanol," which is the
name
that needs to be used in the [molecules] directive below.  But then, too,
you're
not using the same residue name either (MTH instead of MeOH), so it is still
not
possible to say what's going wrong.

-Justin

> [ system ]
> ; Name
> Protein in methanol
>
> [ molecules ]
> ; Compound#mols
> Protein 1
> MTH   660
>

--
==
==

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] Re: Re: methanol simulation error

[Justin A. Lemkul]

mustafa bilsel wrote:

Daer Justin,
I changed the last line as
MTH 660

I got the same error,
Atomtype CMET not found

Do you mean this?



I already explained to you what the problem was with that error:

http://lists.gromacs.org/pipermail/gmx-users/2011-January/057323.html

If you ignore the advice you've been given, you're unlikely to continue to get 
help.  What's more, you keep changing your information.  First, you were using 
"SOL 291" and the error was that there was no such moleculetype, then it was 
"SOL 660" with an atomtype error, then a topology that we suspect has one or 
both of these errors.


If you want free help, here are two tips:

1. Apply what you've been told, and respond directly with whether it did or did 
not work, with relevant output or evidence of a problem.
2. Do not change information mid-stream unless that change was offered to you as 
a potential fix or based on something you discovered to be problematic.  In this 
case, state what you've changed and why.  Otherwise, these threads become a 
jumble of impossibly disjointed information, which does not inspire anyone to 
jump in and help (or continue doing so).


-Justin


best wishes
mustafa




Message: 1
Date: Fri, 07 Jan 2011 07:04:05 -0500
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Re: methanol simulation error
To: Discussion list for GROMACS users >

Message-ID: <4d270135.5000...@vt.edu >
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



mustafa bilsel wrote:



 > ; Include Position restraint file
 > #ifdef POSRES
 > #include "posre.itp"
 > #endif
 >
 > ; Include water topology
 > #include "gromos43a1.ff/methanol.itp"
 >

This topology defines the [moleculetype] name as "Methanol," which is 
the name
that needs to be used in the [molecules] directive below.  But then, 
too, you're
not using the same residue name either (MTH instead of MeOH), so it is 
still not

possible to say what's going wrong.

-Justin

 > [ system ]
 > ; Name
 > Protein in methanol
 >
 > [ molecules ]
 > ; Compound#mols
 > Protein 1
 > MTH   660
 >

--
==
==

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



--


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] Ion-Clustering?

[Micholas Smith]

Hello everyone,I've been performing some rather long simulations (400ns) of a short peptide chain in explicit TIP4P water solvent using opls-aa forcefield with ionic concentrations near 1M, and I am finding a lot of "clustering" of my ionic species. Has anyone else run into this type of problem? I am running NPT with a temperature of 283K with berendsen coupling. For electrostatics iI am using PME, which I have been told works welll with ions in solution. The clustering of the ions reminds me of a crystallization process, this just doesn't feel like it's physical.Thanks in advance.Micholas D. Smith Graduate StudentDrexel University
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Re: [gmx-users] Re: Re: methanol simulation error

[Mark Abraham]

On 8/01/2011 1:09 AM, mustafa bilsel wrote:

Daer Justin,
I changed the last line as
MTH 660

I got the same error,
Atomtype CMET not found

Do you mean this?


Go and look at the molecule name in gromos43a1.ff/methanol.itp and find 
the name it uses. You *must* use that name in the [molecules] section, 
and *nothing* else. Computers are literal, and so must you be if you 
wish to work successfully with them.


However, grompp is breaking before it gets to the stage where the above 
point becomes relevant. You've now been asked twice to try updating 
GROMACS to version 4.5.3 to see if the bug fix Justin remembers is 
applicable to your case. Appearing to silently ignore people's 
suggestions is a great way to get them to silently ignore you :-)


Cheers,

Mark
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Re: [gmx-users] To make continuous trj in REMD

[Justin A. Lemkul]

Qin Qiao wrote:



2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>>



Qin Qiao wrote:



2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu> >>




   Qin Qiao wrote:

   Dear all,

   I came across a problem when I want to make the REMD
   trajectories continuous.

   What I did:

   1. 'demux.pl  
 REMD_0.log' --to get the
'replica_index.xvg'


   2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux
   ../replica_index.xvg'

   It seems smooth. But when I check the rmsd of the output
   0_resort.xtc, I found it's still discontinuous.. with big
jumps
   about 0.5nm..! Could you help me to figure out what's wrong?
   Thanks a lot.


   Have you properly accounted for periodicity effects?

   -Justin


It's the same after I remove periodicity by trjconv -pbc mol -ur
compact ...
 



One iteration of trjconv is not necessarily enough to produce a
properly imaged trajectory.  What is going on in the trajectory when
these spikes are occurring?

-Justin

In VMD, it just seems to change to a different conformation...



Then it sounds like something has gone wrong with the demultiplexing.  As for 
what that is, it's hard to say.  Look into the .log file and resulting .xvg file 
(from demux.pl) to make sure that the proper exchanges were identified.  Then 
try to determine from which replica that sudden change arose (i.e., in which of 
the original trajectories was that configuration present).  Finding it should be 
relatively easy; just dump out the frames at that time point from each of the 
trajectories to see.


For further troubleshooting, it would also be useful to know your Gromacs 
version, in case there is some sort of bug.  It is too early to tell, though, 
where the problem lies.


-Justin


   Best,

   Qin

   -- 

   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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-- 



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] Requesting advice on pressure scaling in a protein-in-membrane system.

[Daniel Adriano Silva M]

Dear gmx users and developers,

I am facing a problem that is new for me and I will appreciate advice from
your expertise. I am working with a big protein complex (around 100K atoms,
several subunits) and I used g_membed to embed it in a (aprox 24 14 nm)
pre-equilibrated POPC membrane, however after embedding and a 1ns of NVT
equilibration I tried to proced to the NPT equilibration, but I found my
system exploding (things moving to fast), so I tried several methods that
came to my mind (like decrease the P-coupling constant, decrease the
timestep and some others). After few tries I went back to the
NVT  equilibration and took a look to the pressure, for my surprise I found
it to be around 1e30! So I ended with a very compressed system on X-Y, I
guess given the embedding of the protein in the membrane. Here are the
questions:

1) Are there any reasonable simple method to reduce the pressure on the
protein/lipid system?
2) May I expect a very long time to reach the adequate pressure and
equilibrium given a possible change on the phase of the lipids by the high
pressure?
3) Any other useful direction?

Extra information: On this step I had frozen the Protein and excluded the
Protein-Protein energy.

Thanks,
Daniel Silva
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Re: [gmx-users] Requesting advice on pressure scaling in a protein-in-membrane system.

[Justin A. Lemkul]

Daniel Adriano Silva M wrote:

Dear gmx users and developers,

I am facing a problem that is new for me and I will appreciate advice 
from your expertise. I am working with a big protein complex (around 
100K atoms, several subunits) and I used g_membed to embed it in a 
(aprox 24 14 nm) pre-equilibrated POPC membrane, however after embedding 
and a 1ns of NVT equilibration I tried to proced to the NPT 
equilibration, but I found my system exploding (things moving to fast), 
so I tried several methods that came to my mind (like decrease the 
P-coupling constant, decrease the timestep and some others). After few 
tries I went back to the NVT  equilibration and took a look to the 
pressure, for my surprise I found it to be around 1e30! So I ended with 
a very compressed system on X-Y, I guess given the embedding of the 
protein in the membrane. Here are the questions:


1) Are there any reasonable simple method to reduce the pressure on the 
protein/lipid system?
2) May I expect a very long time to reach the adequate pressure and 
equilibrium given a possible change on the phase of the lipids by the 
high pressure?

3) Any other useful direction?

Extra information: On this step I had frozen the Protein and excluded 
the Protein-Protein energy.




During NVT?  Turn off this freezing before proceeding, doing additional NVT if 
necessary.  Frozen groups can do weird things, and I would suspect that your 
system simply isn't stable in the presence of these frozen groups.


I have a procedure (and troubleshooting tips) for equilibrating membrane protein 
systems in my tutorial:


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

You may find it useful.  Membrane systems do take a while to converge, but 
that's not your issue here.  You have some fundamental instability to deal with 
first.


-Justin


Thanks,
Daniel Silva



--


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] trjconv with multiple chains

[ms]

On 07/01/11 02:17, yuanyuan wang wrote:

dear all,
  I am doing a simulation that have many chains in a box , and I can 
find a center for them after serval tries.
  I use almost every option of trjconv,-pbc mol,atom,res,whole,nojump , 
-ur compact, -center , -box to got bigger box, and -boxcenter, -fit ..
  still some chain cannot convert into box. them jump from one box to 
another ,
  is there any ways that they not jump to another box?
  thanks a lot.



If they do cluster together fast (like mine), the solution I found -with 
the help of Justin Lemkul, if I remember correctly- was to use trjconv 
for simply centering on one of the chains. This way the aggregate, once 
formed, stayed in the center.


If they just diffuse, I suspect there's nothing you can do: you have 
stuff diffusing in a periodic system, and WYSIWYG.


m.

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[gmx-users] justin

[mustafa bilsel]

Justin,

Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH.

Nothing changed. I suggest you to try it by yourself.
Don't try to remind people the help rules.
JUST HELP OR DONOT HELP.

mustafa


This topology defines the [moleculetype] name as "Methanol," which is the
name
that needs to be used in the [molecules] directive below.  But then, too,
you're
not using the same residue name either (MTH instead of MeOH), so it is still
not
possible to say what's going wrong.

-Justin
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Re: [gmx-users] justin

[Justin A. Lemkul]

mustafa bilsel wrote:

Justin,

Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH.

Nothing changed. I suggest you to try it by yourself.


I did, and it works quite nicely.


Don't try to remind people the help rules.
JUST HELP OR DONOT HELP.



I guess attempting to guide you to more effective posts and faster answers has 
somehow angered you.  Since you're offering me the choice, I choose not to.


-Justin


mustafa


This topology defines the [moleculetype] name as "Methanol," which is 
the name
that needs to be used in the [molecules] directive below.  But then, 
too, you're
not using the same residue name either (MTH instead of MeOH), so it is 
still not

possible to say what's going wrong.

-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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[gmx-users] XTC file not being created, while TRR file is

[João Rodrigues]

Hello all,

I'm trying to run energy minimization on my system (protein complex). Since
it's a bit big (produces 2GB of trr files using l-bfgs) I'm trying to
supress most of this output and replace the trr file with an xtc file.

I'm using these options in my mdp file (output related):

nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy   = 0
nstlog  = 0
nstenergy   = 0
nstxtcout   = 10
xtc-precision   = 1000

Still, I get no xtc file (even if I explicitly run mdrun with the -x option)
and I still get a large trr file.

Am I doing something wrong?

Best!

João Rodrigues
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Re: [gmx-users] XTC file not being created, while TRR file is

[Diego Enry]

Hi João, I don't remember EM runs ever producing .xtc files, maybe to
prevent people to use them when "grompp'ing" in the next step. (they're at
much lower precision)

Anyway, that would be nice in case you want to see what's going on during
EM.


On Fri, Jan 7, 2011 at 7:02 PM, João Rodrigues  wrote:

> Hello all,
>
> I'm trying to run energy minimization on my system (protein complex). Since
> it's a bit big (produces 2GB of trr files using l-bfgs) I'm trying to
> supress most of this output and replace the trr file with an xtc file.
>
> I'm using these options in my mdp file (output related):
>
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstcalcenergy   = 0
> nstlog  = 0
> nstenergy   = 0
> nstxtcout   = 10
> xtc-precision   = 1000
>
> Still, I get no xtc file (even if I explicitly run mdrun with the -x
> option) and I still get a large trr file.
>
> Am I doing something wrong?
>
> Best!
>
> João Rodrigues
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
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Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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[gmx-users] 4. Requesting advice on pressure scaling in a protein-in-membrane system. (Daniel Adriano Silva M)

[Gerrit Groenhof]

Can you simulate the membrane and protein seperately, thus the two system you 
are trying to merge?

Gerrit

> 
>  4. Requesting advice on pressure scaling in a
> protein-in-membrane system. (Daniel Adriano Silva M)
> 


> 
> Dear gmx users and developers,
> 
> I am facing a problem that is new for me and I will appreciate advice from
> your expertise. I am working with a big protein complex (around 100K atoms,
> several subunits) and I used g_membed to embed it in a (aprox 24 14 nm)
> pre-equilibrated POPC membrane, however after embedding and a 1ns of NVT
> equilibration I tried to proced to the NPT equilibration, but I found my
> system exploding (things moving to fast), so I tried several methods that
> came to my mind (like decrease the P-coupling constant, decrease the
> timestep and some others). After few tries I went back to the
> NVT  equilibration and took a look to the pressure, for my surprise I found
> it to be around 1e30! So I ended with a very compressed system on X-Y, I
> guess given the embedding of the protein in the membrane. Here are the
> questions:
> 
> 1) Are there any reasonable simple method to reduce the pressure on the
> protein/lipid system?
> 2) May I expect a very long time to reach the adequate pressure and
> equilibrium given a possible change on the phase of the lipids by the high
> pressure?
> 3) Any other useful direction?
> 
> Extra information: On this step I had frozen the Protein and excluded the
> Protein-Protein energy.
> 
> Thanks,
> Daniel Silva
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110107/b897663b/attachment-0001.html
> 
> --
> 
> Message: 5
> Date: Fri, 07 Jan 2011 10:07:27 -0500
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Requesting advice on pressure scaling in a
>   protein-in-membrane system.
> To: Discussion list for GROMACS users 
> Message-ID: <4d272c2f.2070...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Daniel Adriano Silva M wrote:
>> Dear gmx users and developers,
>> 
>> I am facing a problem that is new for me and I will appreciate advice 
>> from your expertise. I am working with a big protein complex (around 
>> 100K atoms, several subunits) and I used g_membed to embed it in a 
>> (aprox 24 14 nm) pre-equilibrated POPC membrane, however after embedding 
>> and a 1ns of NVT equilibration I tried to proced to the NPT 
>> equilibration, but I found my system exploding (things moving to fast), 
>> so I tried several methods that came to my mind (like decrease the 
>> P-coupling constant, decrease the timestep and some others). After few 
>> tries I went back to the NVT  equilibration and took a look to the 
>> pressure, for my surprise I found it to be around 1e30! So I ended with 
>> a very compressed system on X-Y, I guess given the embedding of the 
>> protein in the membrane. Here are the questions:
>> 
>> 1) Are there any reasonable simple method to reduce the pressure on the 
>> protein/lipid system?
>> 2) May I expect a very long time to reach the adequate pressure and 
>> equilibrium given a possible change on the phase of the lipids by the 
>> high pressure?
>> 3) Any other useful direction?
>> 
>> Extra information: On this step I had frozen the Protein and excluded 
>> the Protein-Protein energy.
>> 
> 
> During NVT?  Turn off this freezing before proceeding, doing additional NVT 
> if 
> necessary.  Frozen groups can do weird things, and I would suspect that your 
> system simply isn't stable in the presence of these frozen groups.
> 
> I have a procedure (and troubleshooting tips) for equilibrating membrane 
> protein 
> systems in my tutorial:
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
> 
> You may find it useful.  Membrane systems do take a while to converge, but 
> that's not your issue here.  You have some fundamental instability to deal 
> with 
> first.
> 
> -Justin
> 
>> Thanks,
>> Daniel Silva
>> 
> 
> -- 
> 
> 
> 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] When will FEP be on GPU?

[Szilárd Páll]

Hi,

Currently there is no concrete plan to implement FEP on GPUs. AFAIK
there is an OpenMM plugin which could be integrated, but I surely
don't have time to work on that and I don't know of anyone else
working on it. Contribution would be welcome, though!

Regards,
--
Szilárd



On Thu, Nov 11, 2010 at 4:49 PM, TJ Mustard  wrote:
> Hi all,
>
>
>
> Our group is doing FEP calculations and finding that we need to run alot of
> simulations for a long time to get accurate results. We would love to see
> FEP on GPU as this would help us increase our computational power without
> buying a new expensive cluster. I would be happy to be a/the guinea pig on
> this one.
>
>
>
> Thank you,
>
> TJ Mustard
> Email: musta...@onid.orst.edu
>
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[gmx-users] Re: XTC file not being created, while TRR file is

[João Rodrigues]

>
> Hi João, I don't remember EM runs ever producing .xtc files, maybe to
>
> prevent people to use them when "grompp'ing" in the next step. (they're at
> much lower precision)
>
> Anyway, that would be nice in case you want to see what's going on during
> EM.
>
>
Thanks for the answer Diego, indeed I thought of that but since my trr file
was not getting any shorter (even with all the options turned off) I thought
there was a mistake. I ended up reducing the size using the exact same
options as above (without xtc part) and using -compact in mdrun. Also, I
think there was an issue with my csh session that was no matter what changes
I did to the mdp file, they were not being reproduced. I reset the terminal
and it worked better. 300MB is better than 2GB :)

Thanks!

João [...] Rodrigues
http://doeidoei.wordpress.com
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Re: [gmx-users] inconsistent energies

[Mark Abraham]

On 8/01/2011 12:10 AM, Vlad Isaev wrote:

Hi,

I want to calculate the energy of a peptide. No minimization, or md, 
just the energy at 0 K. I use this input:


integrator   = steep
nsteps   = 0
nstenergy= 1
nstlist  = 0
ns_type  = simple
pbc  = no
rlist= 0
rcoulomb = 0
rvdw = 0


I get:

Potential Energy  = -1.1744482e+02

Changing steep to cg changes the potential energy even though nsteps=0:

Potential Energy  = -1.2410449e+02

The corresponding energy from AMBER10 is : -1.20172848e+02 (conversion 
factor 4.184).


Any ideas why these are so different?


That's pretty weird. Please double check that you were really using the 
same input coordinates to grompp (and that mdrun wasn't picking up a 
checkpoint file).


Mark
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Re: [gmx-users] Ion-Clustering?

[Mark Abraham]

On 8/01/2011 12:56 AM, Micholas Smith wrote:

Hello everyone,

I've been performing some rather long simulations (400ns) of a short 
peptide chain in explicit TIP4P water solvent using opls-aa forcefield 
with ionic concentrations near 1M, and I am finding a lot of 
"clustering" of my ionic species. Has anyone else run into this type 
of problem? I am running NPT with a temperature of 283K with berendsen 
coupling. For electrostatics iI am using PME, which I have been told 
works welll with ions in solution. The clustering of the ions reminds 
me of a crystallization process, this just doesn't feel like it's 
physical.


That's weird. What's your .mdp file?

Mark
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Re: [gmx-users] g_msd Utility - (Unexpected) Different Results Depending on Output Flag

[Mark Abraham]

On 6/01/2011 2:03 AM, Solomon Berman wrote:

Greetings friends!

I have a question this morning about the g_msd utility related to the output 
generated by different flags.

I'm working with an LJ Liquid and am trying to determine the diffusion constant 
for the system.  I'm employing both the Einstein formulation and the Green Kubo 
formula.  Obviously, for the Einstein equation, I need the mean square 
displacement versus time.  The box I am using is cubic, with a length of a side 
of 3.602 nm.

Now, when I pass the flag -o for an output (to get the data of the MSD of the 
system versus time) with g_msd, and plot the results in xmgrace, I find that 
the slope of the resulting graph continuously increases linearly once in the 
diffusion regime until the end of the simulation time.  However, if I pass the 
flag -mol (to get the average MSD per atom) alongside -o, the curve saturates 
at two-thirds of the maximum mean square displacement and the slope goes to 
zero.

I would like to inquire as to why I receive two different results between "g_msd -o" and 
"g_msd -o -mol"?  In particular, is it possible that the boundary conditions are treated 
differently for each output, where -o ignores the periodic boundary conditions and -mol uses the 
periodic boundary conditions?  I have tried combing the internet, and the man pages, and haven't 
been able to find anything on the reason for the difference in results.


Yes, g_msd -mol leads to a different treatment of periodicity - it 
ensures molecules are whole across periodic boundaries. I have updated 
the g_msd -h text to note this.


Mark
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Re: [gmx-users] justin

[ms]

On 07/01/11 17:00, mustafa bilsel wrote:

Justin,

Are you sure? I installed 4.5.3 and tried Methanol, MTH, MeOH.

Nothing changed. I suggest you to try it by yourself.
Don't try to remind people the help rules.
JUST HELP OR DONOT HELP.


We're not at your orders and shouting at people who try to help you is 
unbelievably rude. Therefore, in any case, with you I'll choose the 
second option. Bye, you're going in my spam folder.


m.



mustafa


This topology defines the [moleculetype] name as "Methanol," which is the
name
that needs to be used in the [molecules] directive below.  But then, too,
you're
not using the same residue name either (MTH instead of MeOH), so it is still
not
possible to say what's going wrong.

-Justin





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[gmx-users] Re: inconsistent energies

[Vlad Isaev]

Thanks, Mark.

No, it is not picking any chk files. But the coordinates in the gro file
after mdrun change slightly for some of the atoms on using cg and l-bfgs,
whereas with steep they remain the same.

e.g., in b4min.gro submitted to cg or l-bfgs or steep:

2GLY  O   13   0.736   0.922  -0.350

in min.gro after cg and l-bfgs:

 2GLY  O   13   0.735   0.920  -0.349

in min.gro after steep:

2GLY  O   13   0.736   0.922  -0.350

So, I guess I have to trust steep on this if I just need the energy of the
molecule as the coordinates of atoms do not change.

By the look of it, AMBER10 also changes coordinates slightly on using:

 imin=0, maxcyc = 0, ncyc = 0, ntb = 0, cut = 9

Is there any other way of calculating a single point energy by GROMACS?

-Vlad

On 8/01/2011 12:10 AM, Vlad Isaev wrote:

>* Hi,
*>*
*>* I want to calculate the energy of a peptide. No minimization, or md,
*>* just the energy at 0 K. I use this input:
*>*
*>* integrator   = steep
*>* nsteps   = 0
*>* nstenergy= 1
*>* nstlist  = 0
*>* ns_type  = simple
*>* pbc  = no
*>* rlist= 0
*>* rcoulomb = 0
*>* rvdw = 0
*>*
*>*
*>* I get:
*>*
*>* Potential Energy  = -1.1744482e+02
*>*
*>* Changing steep to cg changes the potential energy even though nsteps=0:
*>*
*>* Potential Energy  = -1.2410449e+02
*>*
*>* The corresponding energy from AMBER10 is : -1.20172848e+02 (conversion
*>* factor 4.184).
*>*
*>* Any ideas why these are so different?
*
< That's pretty weird. Please double check that you were really using the
< same input coordinates to grompp (and that mdrun wasn't picking up a
< checkpoint file).

< Mark
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Re: [gmx-users] Re: inconsistent energies

[Mark Abraham]

On 8/01/2011 1:38 PM, Vlad Isaev wrote:

Thanks, Mark.

No, it is not picking any chk files. But the coordinates in the gro 
file after mdrun change slightly for some of the atoms on using cg and 
l-bfgs, whereas with steep they remain the same.


OK, well this must be a consequence of the algorithms, despite being 
zero-step.




e.g., in b4min.gro submitted to cg or l-bfgs or steep:

2GLY  O   13   0.736   0.922  -0.350

in min.gro after cg and l-bfgs:

 2GLY  O   13   0.735   0.920  -0.349

in min.gro after steep:

2GLY  O   13   0.736   0.922  -0.350

So, I guess I have to trust steep on this if I just need the energy of 
the molecule as the coordinates of atoms do not change.


By the look of it, AMBER10 also changes coordinates slightly on using:

 imin=0, maxcyc = 0, ncyc = 0, ntb = 0, cut = 9

Is there any other way of calculating a single point energy by GROMACS?


There's zero-step MD, so long as you make sure the start is 
unconstrained. The mdrun -rerun functionality does single point energies 
over a trajectory, which can be one configuration. By definition, the 
latter doesn't change configurations.


Mark



-Vlad

On 8/01/2011 12:10 AM, Vlad Isaev wrote:
>/  Hi,
/>/
/>/  I want to calculate the energy of a peptide. No minimization, or md,
/>/  just the energy at 0 K. I use this input:

/>/
/>/  integrator   = steep
/>/  nsteps   = 0
/>/  nstenergy= 1
/>/  nstlist  = 0
/>/  ns_type  = simple

/>/  pbc  = no
/>/  rlist= 0
/>/  rcoulomb = 0
/>/  rvdw = 0
/>/
/>/
/>/  I get:

/>/
/>/  Potential Energy  = -1.1744482e+02
/>/
/>/  Changing steep to cg changes the potential energy even though nsteps=0:
/>/
/>/  Potential Energy  = -1.2410449e+02

/>/
/>/  The corresponding energy from AMBER10 is : -1.20172848e+02 (conversion
/>/  factor 4.184).
/>/
/>/  Any ideas why these are so different?
/
<  That's pretty weird. Please double check that you were really using the

<  same input coordinates to grompp (and that mdrun wasn't picking up a
<  checkpoint file).

<  Mark



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