Re: [gmx-users] Segmentation Fault using g_cluster

[Mark Abraham]

On 28/03/2012 2:14 PM, Davide Mercadante wrote:
Thank you for the prompt reply.! Indeed, I am using Gromacs version 
4.5.5 compiled in double-precision and I am running the analysis on a 
MacBook PRO.


I tried to open an issue at http://redmine/gromacs.org but it asks me 
for login name and passwd which I don't think I have as I never 
subscribed as developer. I may be wrong though..do I need to register?


Yes, just sign up. We need to be able to contact you to let you know the 
solution or get more information, so anonymous bug submission is not 
very useful.


I suppose that if this is not an explainable issue at the moment there 
is no solution to it?


The problem with plain segfaulting is that there's no way to tell what 
caused the problem. GROMACS tries hard not to do this, but clearly it's 
not perfect. There may be a code bug. There may be a way for you to use 
the code better. We just don't know yet. There's certainly room to 
improve the code.


Mark



Thank you again for the reply. It has been much appreciated.

Davide

From: Mark Abraham >
Reply-To: Discussion list for GROMACS users >

Date: Wed, 28 Mar 2012 13:29:40 +1100
To: Discussion list for GROMACS users >

Subject: Re: [gmx-users] Segmentation Fault using g_cluster

On 28/03/2012 1:00 PM, Davide Mercadante wrote:

Dear Gromacs Users,

I am trying to run g_cluster to find an average structure for my 
system and after giving the following command line:


g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb 
-n --g


g_cluster started without problems and continued calculating the 
matrix etc...until I got this:


Last frame   5000 time 5.004
Allocated 645448320 bytes for frames
Read 5001 frames from trajectory allnj10_XM10.xtc
Computing 5001x5001 RMS deviation matrix
# RMSD calculations left: 0

The RMSD ranges from 0.0816802 to 0.301369 nm
Average RMSD is 0.208468
Number of structures for matrix 5001
Energy of the matrix is 364.532 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802
Linking structures **
Sorting and renumbering clusters

Found 1425 clusters

Writing middle structure for each cluster to pdb_ligplot_XM.pdb
Segmentation fault: 11

Can you please help me to understand where the problem comes from and 
how I can solve it?

Any help is greatly appreciated.


I don't think this should happen. You haven't stated your GROMACS 
version. If you can reproduce this with 4.5.5., please open an issue 
here http://redmine.gromacs.org/ and upload your files and 
instructions on how to reproduce the problem.


Mark
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[gmx-users] Position restraints problem

[Jernej Zidar]

Hi.
  After successfully importing a CHARMM-generated PDB file to GROMACS
I set out to do some short simulations. While all calculations
finished without a problem if everything but the water molecules were
fixed.

  Removing the position restraints led to the system blowing up. Using
J. Lemkul's tutorial suggestion I generated an index file selecting
one lipid atom from sphingomyelin and one from cholesterol using
make_ndx and the selection: a P | a O3 (alternatively I tried also "6
| 7 | 17 | 18 | a P | a O3"). Any of the two selections selects only
atoms from the lipid part of the system.

  After creating the index file I used genrestr to position restrain
the movements of the selected atoms and obtain a position restrain ITP
file. I included this ITP file at the end of the lipid topology ITP
file as instructed on GROMACS' website.

 In the last step I edited the MDP file to use the position restraints
file for some lipid atoms but something went wrong as GROMPP
complains:
Fatal error:
[ file sys9-tmp-ions-mini-nofix-2-posre.itp, line 116 ]:
Atom index (12014) in position_restraints out of bounds (1-11954).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

  Indeed, checking the lipid ITP file revealed there is no atom index
12014, yet there is an atom index 12014 (with the proper name) in the
GRO file (that I used to create both the index and the restraints
file) where all the atoms are listed. What have I done wrong?

Thanks advance,
Jernej Zidar
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Re: [gmx-users] Position restraints problem

[Mark Abraham]

On 28/03/2012 6:52 PM, Jernej Zidar wrote:

Hi.
   After successfully importing a CHARMM-generated PDB file to GROMACS
I set out to do some short simulations. While all calculations
finished without a problem if everything but the water molecules were
fixed.

   Removing the position restraints led to the system blowing up. Using
J. Lemkul's tutorial suggestion I generated an index file selecting
one lipid atom from sphingomyelin and one from cholesterol using
make_ndx and the selection: a P | a O3 (alternatively I tried also "6
| 7 | 17 | 18 | a P | a O3"). Any of the two selections selects only
atoms from the lipid part of the system.

   After creating the index file I used genrestr to position restrain
the movements of the selected atoms and obtain a position restrain ITP
file. I included this ITP file at the end of the lipid topology ITP
file as instructed on GROMACS' website.

  In the last step I edited the MDP file to use the position restraints
file for some lipid atoms but something went wrong as GROMPP
complains:
Fatal error:
[ file sys9-tmp-ions-mini-nofix-2-posre.itp, line 116 ]:
Atom index (12014) in position_restraints out of bounds (1-11954).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

   Indeed, checking the lipid ITP file revealed there is no atom index
12014, yet there is an atom index 12014 (with the proper name) in the
GRO file (that I used to create both the index and the restraints
file) where all the atoms are listed. What have I done wrong?


See the warning in genrestr -h.

If all you're doing is adding a single atom of position restraint per 
moleculetype, you can do that by hand faster than using make_ndx and 
genrestr and adding the #include.


Mark
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[gmx-users] Re: gmx-users Digest, Vol 95, Issue 175

[Song Ke]

On Wed, March 28, 2012 00:53, gmx-users-requ...@gromacs.org wrote:
> Send gmx-users mailing list submissions to
>   gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>   gmx-users-requ...@gromacs.org
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>   gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: WHAM question (lloyd riggs)
>2. Re: WHAM2 (lloyd riggs)
>3. Re: amber99sb_virtual site lipids dopc MCH3_N constraint
>   types (Mark Abraham)
>4. Re: dssp error (Mark Abraham)
>5. Re: Vi plugin for Gromacs files (Szil?rd P?ll)
>6. Re: Re: How to add dihedral information from the GAFF
>   topology (bipin singh)
>
>
> --
>
> Message: 1
> Date: Tue, 27 Mar 2012 16:45:55 +0200
> From: "lloyd riggs" 
> Subject: [gmx-users] Re: WHAM question
> To: jalem...@vt.edu, Discussion list for GROMACS users
>   
> Message-ID: <20120327144555.30...@gmx.net>
> Content-Type: text/plain; charset="utf-8"
>
> Quick question to anyone,
>
> can you extract energies and forces with g_traj and g_energy and feed them
> to WHAM for molecule by molecule or atom by atom PMF determination.  If
> so, how do I get WHAM to read the extracted enrgies as they are written
> out.  I did read something about a .pdo file if you have wierdness, that
> it could be used from the past?
>
> Explanation:  WHAM works fine for my system, and gives nice curves and
> expected values, however when I try and do this for say a particular amino
> acid by hand the values expected vary. I most likely am just screwing the
> sums (ive been using every term including rest) or theres a difference
> between WHAM and my means of doing the free energy change?  I want to stay
> uniform.
>
> Any help or suggestions appriciated
>
> Sincerely
>
> Stephan Watkins
>
>
> --
> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!
> Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a
>
>
> --
>
> Message: 2
> Date: Tue, 27 Mar 2012 16:56:25 +0200
> From: "lloyd riggs" 
> Subject: [gmx-users] Re: WHAM2
> To: jalem...@vt.edu, Discussion list for GROMACS users
>   
> Message-ID: <20120327145625.83...@gmx.net>
> Content-Type: text/plain; charset="utf-8"
>
>
> Another WHAM question,
>
> If I use the pullx (position) Vs the pullf(force) i get differ4ent graphs
> but the same overall delG (or PMF).
>
> in the positional one it is a juttery line then at the break point (when
> the protein finally lets go enough) it jumps up to almost its maximum.
> When I use the Force, its a nice smooth graph as from the tutorials?  I
> could in reference to the last e-mail use a positional pullx for each
> amino acid, but then this gives a table (which is all I really need) but
> still varies (1-2 kCal/mol for some adding up in the end to alot say 10-15
> kCal/mol or >10% STDDEV)
>
> Stephan
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>
>
> --
>

There is no constraints for the virtual site (CH3)3-N bond in amber
ffbonded.itp in gromacs . And it is important in capped proteins and
lipids virtual site.

Song

> Message: 3
> Date: Wed, 28 Mar 2012 03:20:36 +1100
> From: Mark Abraham 
> Subject: Re: [gmx-users] amber99sb_virtual site lipids dopc MCH3_N
>   constraint  types
> To: Discussion list for GROMACS users 
> Message-ID: <4f71e8d4.9090...@anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 27/03/2012 11:54 PM, Song Ke wrote:
>> Dear All,
>>
>> I have a question about create and simulate dopc lipid virtual sites. I
>> noticed in ffbonded.itp
>>
>> [ constrainttypes ]
>> ; this section is implemented manually from bond&  angle values
>>
>> ; constraints for rigid CH3 groups
>>   MCH3   CT  20.166426
>>   MCH3   S   20.193875
>>   MCH3   MCH320.092163
>> ; constraints for rigid NH3 groups
>>   MNH3   CT  20.158254
>>   MNH3   MNH320.080229
>>
>> ; angle-derived constraints for OH and SH groups in proteins
>> ; The constraint A-C is calculated from the angle A-B-C and bonds A-B,
>> B-C.
>>C HO  20.195074
>>CAHO  20.195074
>>CTHO  20.194132
>>CTHS  20.235935
>>
>>
>> However, there is no MCH3 N constraint types, how can I get this value?
>>
>> Meanwhile, Is there a website or scripts to generate the dopc virtual
>> sites bonded itp instead of do it manually?
>
> What's unsatisfactory about pdb2gmx -vsite?
>
> Mark
>
>
> --
>
> Message: 4
> Date: Wed, 28 Mar 2012 03:21:48 +1100
> From

[gmx-users] Where would I find the 45A4 GROMOS force field?

[Marc Gordon]

Hi all

I have never posted to the mailing list before but it has proven very
helpful in the past.

I'm looking for the 45A4 force field. I've been asking Mr. Google but so
far I haven't had any luck locating it. This is I imagine probably down to
the wrong keywords or something

 I want to do some work on disaccharides and I would very much like to use
this force field. I'm going to be using it thorugh NAMD.

I thought this would be the best place to ask if anyone knew of a site
where this force field was being maintained or something.


Regards
Marc
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[gmx-users] Position restraints problem

[Jernej Zidar]

On Wed, Mar 28, 2012 at 16:17,   wrote:
> See the warning in genrestr -h.
>
> If all you're doing is adding a single atom of position restraint per
> moleculetype, you can do that by hand faster than using make_ndx and
> genrestr and adding the #include.
>
> Mark

This in turn means genrestr is useless if one has more than one
molecule type. While I could set the restraints manually,
doing it by hand is not really an option if one has more than 100
entries. Ah well, bash magic to the rescue.

Thanks,
Jernej Zidar

For posterity reasons here's the warning:
WARNING: position restraints only work for the one molecule at a time.
Position restraints are interactions within molecules, therefore they should
be included within the correct [ moleculetype ] block in the topology. Since
the atom numbers in every moleculetype in the topology start at 1 and the
numbers in the input file for genrestr number consecutively from 1, genrestr
will only produce a useful file for the first molecule.
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Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

[bipin singh]

Thanks for your inputs.

I have checked the coordinate file thoroughly and the order of atoms
are same as defined in the [molecules] directive.
I really do not able to find out the source of the error.

On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul  wrote:
>
>
> Biswajit Gorai wrote:
>>
>> Dear Bipin,
>> Edit your topology file as:
>>
>> ###
>> ; Include forcefield parameters
>> #include "amber99sb-ildn.ff/forcefield.itp"
>>
>> ; Include chain topologies
>> #include "topol_Protein_chain_A.itp"
>> #include "topol_Ion_chain_A2.itp"
>>
>> *#include "oct.itp"*
>>
>
> If oct.itp introduces new atom types (as the original .top does, for GAFF),
> placing this topology here will result in a fatal error since there is a new
> [atomtypes] directive that is introduced after the protein [moleculetype].
>  If oct.itp does not introduce any new atom types, its location within the
> system topology is irrelevant.
>
>> ; Include water topology
>> #include "amber99sb-ildn.ff/tip3p.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 "amber99sb-ildn.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> Ion_chain_A2        1
>> *1-octanol         1
>> *
>> *SOL              8987*
>
>
> Depending on the order of the coordinate file, it may not be possible to
> merge the SOL entries in this way.
>
> -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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-- 
---
Regards,
Bipin Singh
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[gmx-users] on MD at constant pH

[Acoot Brett]

Dear All,

Currently is it possible to run MD at a constant pH value?

I am looking forward to getting a reply from you.

Cheers,

Acoot
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[gmx-users] calculation Tm of the protein by GROMACS

[Acoot Brett]

Dear All,

Can you show me a webpage to calculate the Tm (melting temperature) of a 
protein (complex) by Gromacs?

Cheers,

Acoot
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Re: [gmx-users] on MD at constant pH

[Justin A. Lemkul]

Acoot Brett wrote:


Dear All,

Currently is it possible to run MD at a constant pH value?



The concept of pH is not well defined in MD simulations.  In normal MD, you 
can't transfer protons and you can't explicitly model the actual hydronium 
concentration without making your box unreasonably large (which also assumes 
there are parameters in your chosen force field for H3O+).


There are, of course, constant pH methods, but they are not implemented in 
Gromacs.  There is extensive discussion of these topics in the list archive.


At present, you can model a constant protonation state of your molecule.  You 
should not, of course, equate this with a true "constant pH," but the model is 
often used.  You can assign your molecule the predominant protonation state at a 
given pH.


-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] Re: How to add dihedral information from the GAFF topology

[Justin A. Lemkul]

bipin singh wrote:

Thanks for your inputs.

I have checked the coordinate file thoroughly and the order of atoms
are same as defined in the [molecules] directive.
I really do not able to find out the source of the error.



Looking closer at the error, what's happening is your octanol molecule is in a 
place where the topology expects the amino acid sequence Ser-Leu.  Perhaps that 
will help you track down the source of the problem.  It seems to me that your 
octanol molecule occurs earlier in the coordinate file than it does in the topology.


If you still can't locate the problem, then you can always start over building 
your system in a known order, checking the alignment of the coordinate file and 
topology at every step.


-Justin


On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul  wrote:


Biswajit Gorai wrote:

Dear Bipin,
Edit your topology file as:

###
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Ion_chain_A2.itp"

*#include "oct.itp"*


If oct.itp introduces new atom types (as the original .top does, for GAFF),
placing this topology here will result in a fatal error since there is a new
[atomtypes] directive that is introduced after the protein [moleculetype].
 If oct.itp does not introduce any new atom types, its location within the
system topology is irrelevant.


; Include water topology
#include "amber99sb-ildn.ff/tip3p.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 "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Ion_chain_A21
*1-octanol 1
*
*SOL  8987*


Depending on the order of the coordinate file, it may not be possible to
merge the SOL entries in this way.

-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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--


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] Where would I find the 45A4 GROMOS force field?

[Justin A. Lemkul]

Marc Gordon wrote:

Hi all

I have never posted to the mailing list before but it has proven very 
helpful in the past.


I'm looking for the 45A4 force field. I've been asking Mr. Google but so 
far I haven't had any luck locating it. This is I imagine probably down 
to the wrong keywords or something


 I want to do some work on disaccharides and I would very much like to 
use this force field. I'm going to be using it thorugh NAMD.


I thought this would be the best place to ask if anyone knew of a site 
where this force field was being maintained or something.




You can get the files from ATB:

http://compbio.biosci.uq.edu.au/atb/

They are formatted for use with the GROMOS MD package, but that's the only 
source of these files of which I'm aware.


-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] a question related to REMD

[Acoot Brett]

Dear All,

In "http://www.gromacs.org/Documentation/How-tos/REMD";, the first sentence is 
"Replica-Exchange Molecular Dynamics (REMD) is a technique used to enhance 
sampling relative to a standard molecular dynamics simulations by allowing 
systems of similar potential energies to sample 
conformations at different temperatures. By doing so, energy barriers on the 
potential energy surface might be overcome, allowing for the 
exploration of new conformational space."

It sepcifically mentioned "by allowing systems of similar potential energies to 
sample 
conformations at different temperatures". What I want to know is that at 
different temperature, protein can have extremely different potential energies, 
thus how the REMD gurantees "similar potential energies"?

I am looking forward to getting a reply from you.

Cheers,

Acoot
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[gmx-users] on the force field

[Acoot Brett]

Dear All,

Does anyone can make an introduction on the differences among the following 
force fields for protein? Which are much easy to be accepted for publication 
purpose?

Cheers,

Acoot

1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 
2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (with CMAP) - version 2.0
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR-- 
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Re: [gmx-users] on the force field

[David van der Spoel]

On 2012-03-28 13:02, Acoot Brett wrote:


Dear All,

Does anyone can make an introduction on the differences among the
following force fields for protein? Which are much easy to be accepted
for publication purpose?


Try reading some literature. Search for protein force field simulation.



Cheers,

Acoot

  1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
  2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
  3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
  4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
  5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
  6: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 
2010)
  7: AMBERGS force field (Garcia&
  Sanbonmatsu, PNAS 99, 2782-2787, 2002)
  8: CHARMM27 all-atom force field (with CMAP) - version 2.0
  9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR







--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] a question related to REMD

[Justin A. Lemkul]

Acoot Brett wrote:


Dear All,

In "http://www.gromacs.org/Documentation/How-tos/REMD";, the first 
sentence is "Replica-Exchange Molecular Dynamics (REMD) is a technique 
used to enhance sampling relative to a standard molecular dynamics 
simulations 
 
by allowing systems of similar potential energies to sample 
conformations at different temperatures. By doing so, energy barriers on 
the potential energy surface might be overcome, allowing for the 
exploration of new conformational space."


It sepcifically mentioned "by allowing systems of similar potential 
energies to sample conformations at different temperatures". What I want 
to know is that at different temperature, protein can have extremely 
different potential energies, thus how the REMD gurantees "similar 
potential energies"?




The potential energy is calculated for each system from all the normal equations 
and then a probability of exchange is calculated at the exchange interval 
according to the equation given in manual section 3.13.


-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] Principal Components Analysis in Gromacs

[James Starlight]

Dear Gromacs Users!



I have some questions about PCA implemented in Gromacs.


1- I want to increase amplitude of the motions seen on the selected PCs but
I can't found scalling factor option for that.


2- I have calculated MD trajectory for my protein. From this trajectory I
want to find some relevant motions by means of PCA analysis. Also I have
dataset of the experimental structures of that protein where this motion
also presents ( e.g active and innactive conformations of my protein
included in my dataset) As the consequence I want to compare overal
direction of the motion observed along some PCs calculated from MD
trajectory ( it's called EDA) with the motion observed olong other PCs wich
was calculated from the enssemble of the pdb structures. As I've noticed
via  g_anaeig I can compare such datasets by means of -v and -v2 flaggs.
For this purpose I must make trajectory for my X-ray structures at first
and load it with the MD trajectory into the g_anaeig -v md.trr -v2
x_ray.trr. Would this aproach be correct in general ? What should I do if
both of my datasets consist of different number of backbone atoms (due to
some missing residues in the X-ray data) ?


Thanks for help,


James
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,

This sounds like I use very small forces but expect reasonable effect. But
I've applied different forces with step-by-step increasing of force
constants ( from very softest comparable with the thermal motion ( 0.1 kj
mol nm-2) to relatively hight (10).  As the consequence I've observed
effect of application of that harmonic constraints wich I've defined in the
r0 and r1 range but in some case ( where forses were were hight I've seen
perturbation of my structures) and when constraints were low ( in
accordance to my literature) I've not seen desired effect like the
selection of the constraints was wrong ( but actually all restraints were
applied on the correct possitions). This was seen by measurement of the
distances between atom pairs wich were contrained. Eg If I define this
distances in the 0.1написал:

> If there's a car at the bottom of one valley in the Alps, and you think it
> should be two valleys over, and you pull it with a trained cat... it's not
> going to move much. How big an animal you need depends on the geography.
> There need not even be a reasonable route for you to take, if the target
> valley is effectively on Mars.
>
> Mark
>
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Re: [gmx-users] Position restraints problem

[Mark Abraham]

On 28/03/2012 7:39 PM, Jernej Zidar wrote:

On Wed, Mar 28, 2012 at 16:17,  wrote:

See the warning in genrestr -h.

If all you're doing is adding a single atom of position restraint per
moleculetype, you can do that by hand faster than using make_ndx and
genrestr and adding the #include.

Mark

This in turn means genrestr is useless if one has more than one
molecule type. While I could set the restraints manually,
doing it by hand is not really an option if one has more than 100
entries. Ah well, bash magic to the rescue.


It's pretty rare to have more than a handful of [moleculetype] sections, 
each of which would want customized [position_restraints]. pdb2gmx will 
write all-heavy-atom [position_restraints] sections which serve most 
purposes. It would not be hard to modify genrestr to be useful in the 
general case, but until a developer needs it badly enough, it'll be a 
low priority :-)


Mark



Thanks,
Jernej Zidar

For posterity reasons here's the warning:
WARNING: position restraints only work for the one molecule at a time.
Position restraints are interactions within molecules, therefore they should
be included within the correct [ moleculetype ] block in the topology. Since
the atom numbers in every moleculetype in the topology start at 1 and the
numbers in the input file for genrestr number consecutively from 1, genrestr
will only produce a useful file for the first molecule.


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Re: [gmx-users] on MD at constant pH

[Mark Abraham]

On 28/03/2012 9:42 PM, Justin A. Lemkul wrote:



Acoot Brett wrote:


Dear All,

Currently is it possible to run MD at a constant pH value?



The concept of pH is not well defined in MD simulations.  In normal 
MD, you can't transfer protons and you can't explicitly model the 
actual hydronium concentration without making your box unreasonably 
large (which also assumes there are parameters in your chosen force 
field for H3O+).


There are, of course, constant pH methods, but they are not 
implemented in Gromacs.  There is extensive discussion of these topics 
in the list archive.


...and at 
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation


Mark




At present, you can model a constant protonation state of your 
molecule.  You should not, of course, equate this with a true 
"constant pH," but the model is often used.  You can assign your 
molecule the predominant protonation state at a given pH.


-Justin



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Re: [gmx-users] Generation of the Distance Restraints

[Mark Abraham]

On 28/03/2012 10:48 PM, James Starlight wrote:

Mark,

This sounds like I use very small forces but expect reasonable effect. 
But I've applied different forces with step-by-step increasing of 
force constants ( from very softest comparable with the thermal motion 
( 0.1 kj mol nm-2) to relatively hight (10).  As the consequence I've 
observed effect of application of that harmonic constraints wich I've 
defined in the r0 and r1 range but in some case ( where forses were 
were hight I've seen perturbation of my structures) and when 
constraints were low ( in accordance to my literature) I've not seen 
desired effect like the selection of the constraints was wrong ( but 
actually all restraints were applied on the correct possitions). This 
was seen by measurement of the distances between atom pairs wich were 
contrained. Eg If I define this distances in the 0.1r1=0,4 for this instance) range the real distance between i and j 
atoms in the simulated structure was lower or higher of the defined 
range.


What's reasonable depends on the objective. If you want to keep 
something very close to where it *already* is, and it's reasonably happy 
there already, then you don't generally need much in the way of 
restraints. If your starting configurations are different from what you 
wish to achieve, then you're going to have to metaphorically speak loud 
enough to be heard over the thermal commotion, and then loud enough to 
cross the relevant barriers. That can mean big restraint forces and tiny 
integration steps and lots of tweaking and praying. Or finding a new 
starting configuration that's more relevant for the objective.


For comparison, pdb2gmx generations position restraints with 1000 kJ mol 
nm-2 force constants for helping people not perturb their structures 
during equilibration. Your distance deviations are much larger than will 
usually occur with PR, so you don't want to go that large.




By the way I've found that besides such harmonic restraining also I 
can apply more rigid holo restraints from specified value. Could you 
tell me where I could find information of the application of such 
restraints in the topology of my protein? As I understood this could 
be done by means of editing of the bond enty in topology but what 
exactly specified type should I applied on the restried atoms?


Rigid constraints are not useful for you, because your initital 
conditions are a long way from your target conditions. Any kind of 
harmonic potential has the same or worse issues than you already have.


Mark




Thank for help again,

James

22 ? 2012 ?. 17:32  Mark Abraham 
mailto:mark.abra...@anu.edu.au>> ???:


If there's a car at the bottom of one valley in the Alps, and you
think it should be two valleys over, and you pull it with a
trained cat... it's not going to move much. How big an animal you
need depends on the geography. There need not even be a reasonable
route for you to take, if the target valley is effectively on Mars.

Mark

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Re: [gmx-users] Principal Components Analysis in Gromacs

[Tsjerk Wassenaar]

Hi James,

> 1- I want to increase amplitude of the motions seen on the selected PCs but
> I can't found scalling factor option for that.

The analysis gives you the amplitudes that are in your trajectory. Why
do you want to amplify them to something probably non-physical?

>
> 2- I have calculated MD trajectory for my protein. From this trajectory I
> want to find some relevant motions by means of PCA analysis. Also I have
> dataset of the experimental structures of that protein where this motion
> also presents ( e.g active and innactive conformations of my protein
> included in my dataset) As the consequence I want to compare overal
> direction of the motion observed along some PCs calculated from MD
> trajectory ( it's called EDA) with the motion observed olong other PCs wich
> was calculated from the enssemble of the pdb structures. As I've noticed
> via  g_anaeig I can compare such datasets by means of -v and -v2 flaggs. For
> this purpose I must make trajectory for my X-ray structures at first and
> load it with the MD trajectory into the g_anaeig -v md.trr -v2 x_ray.trr.
> Would this aproach be correct in general ? What should I do if both of my
> datasets consist of different number of backbone atoms (due to some missing
> residues in the X-ray data) ?

You have to make sure that the trajectories and the eigenvectors
match. Then you have to think of what you want to do.

- If you want to project the x-ray structures onto the eigenvectors
from the MD simulations, you have to use

g_anaeig -v eigenvec_from_md.trr -s reference.tpr -f xray_structures.pdb -proj

- If you want to compare the similarity of the eigenvectors obtained
from MD and from your crystal structures, you have to do PCA on both
sets separately and then

g_anaeig -v eigenvec_from_md.trr -v2 eigenvec_from_xray.trr -eig
eigenval_from_md.xvg -eig2 eigenval_from_xray.xvg -s reference.tpr
-inpr

Cheers,

Tsjerk

>
>
> Thanks for help,
>
>
> James
>
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-- 
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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] Where would I find the 45A4 GROMOS force field?

[Marc Gordon]

Oh awesome. Thanks so much for this.

I've never worked with GROMOS or gromacs themselves. I'm going to need to
look up whether or not it is possible to use these files to generate files
in the gromacs format required as input for NAMD now but at least having
access to the force fields puts me that much further along. I don't suppose
you know offhand whether such a thing is possible?

I see they have a myriad of force fields available on ATB including the
other one I am interested in 53A6.

Thanks again.


On Wed, Mar 28, 2012 at 2:50 PM, Justin A. Lemkul  wrote:

>
>
> Marc Gordon wrote:
>
>> Hi all
>>
>> I have never posted to the mailing list before but it has proven very
>> helpful in the past.
>>
>> I'm looking for the 45A4 force field. I've been asking Mr. Google but so
>> far I haven't had any luck locating it. This is I imagine probably down to
>> the wrong keywords or something
>>
>>  I want to do some work on disaccharides and I would very much like to
>> use this force field. I'm going to be using it thorugh NAMD.
>>
>> I thought this would be the best place to ask if anyone knew of a site
>> where this force field was being maintained or something.
>>
>>
> You can get the files from ATB:
>
> http://compbio.biosci.uq.edu.**au/atb/
>
> They are formatted for use with the GROMOS MD package, but that's the only
> source of these files of which I'm aware.
>
> -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] Where would I find the 45A4 GROMOS force field?

[Justin A. Lemkul]

Marc Gordon wrote:

Oh awesome. Thanks so much for this.

I've never worked with GROMOS or gromacs themselves. I'm going to need 
to look up whether or not it is possible to use these files to generate 
files in the gromacs format required as input for NAMD now but at least 
having access to the force fields puts me that much further along. I 
don't suppose you know offhand whether such a thing is possible?




Sorry, but I don't.  I haven't done anything with NAMD that wasn't out of the 
box.  That's probably a question better posed to the NAMD people.


-Justin

I see they have a myriad of force fields available on ATB including the 
other one I am interested in 53A6.


Thanks again.


On Wed, Mar 28, 2012 at 2:50 PM, Justin A. Lemkul > wrote:




Marc Gordon wrote:

Hi all

I have never posted to the mailing list before but it has proven
very helpful in the past.

I'm looking for the 45A4 force field. I've been asking Mr.
Google but so far I haven't had any luck locating it. This is I
imagine probably down to the wrong keywords or something

 I want to do some work on disaccharides and I would very much
like to use this force field. I'm going to be using it thorugh NAMD.

I thought this would be the best place to ask if anyone knew of
a site where this force field was being maintained or something.


You can get the files from ATB:

http://compbio.biosci.uq.edu.__au/atb/


They are formatted for use with the GROMOS MD package, but that's
the only source of these files of which I'm aware.

-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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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: How to add dihedral information from the GAFF topology

[Justin A. Lemkul]

bipin singh wrote:

Thanks again



For the record, I didn't ask that you send me your files so I could troubleshoot 
for you.  Luckily for you I'm in a charitable mood this morning, so I took a look ;)


Your problem is that you have a [molecules] directive in oct.itp.  Please refer 
to the documentation for the difference between a .top topology and a .itp topology:


http://www.gromacs.org/Documentation/File_Formats/.itp_File

The presence of this [molecules] directive tells grompp that the first thing it 
should expect is a block of octanol, when in fact your coordinate file has the 
protein first (starting with Ser-Leu, as I suspected).  You then have "1-octanol 
1" in your topol.top, which says you're including another random octanol 
molecule somewhere later.


You need a single [molecules] directive in the .top, which must match the order 
of the coordinate file.  Once you've got that, things should work fine.


-Justin


From the error It seems that I have placed the octane molecule before

the protein but it is not the case, I dont know why grompp is reading
parameters for octane first and expecting it to match with protein. I
know that its my problem and I have to think about
that but just for the reference for you I am attaching the coordinate
and topology files.

On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul  wrote:


bipin singh wrote:

Thanks for your inputs.

I have checked the coordinate file thoroughly and the order of atoms
are same as defined in the [molecules] directive.
I really do not able to find out the source of the error.


Looking closer at the error, what's happening is your octanol molecule is in
a place where the topology expects the amino acid sequence Ser-Leu.  Perhaps
that will help you track down the source of the problem.  It seems to me
that your octanol molecule occurs earlier in the coordinate file than it
does in the topology.

If you still can't locate the problem, then you can always start over
building your system in a known order, checking the alignment of the
coordinate file and topology at every step.

-Justin



On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul  wrote:


Biswajit Gorai wrote:

Dear Bipin,
Edit your topology file as:

###
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Ion_chain_A2.itp"

*#include "oct.itp"*


If oct.itp introduces new atom types (as the original .top does, for
GAFF),
placing this topology here will result in a fatal error since there is a
new
[atomtypes] directive that is introduced after the protein
[moleculetype].
 If oct.itp does not introduce any new atom types, its location within
the
system topology is irrelevant.


; Include water topology
#include "amber99sb-ildn.ff/tip3p.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 "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Ion_chain_A21
*1-octanol 1
*
*SOL  8987*


Depending on the order of the coordinate file, it may not be possible to
merge the SOL entries in this way.

-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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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 | (5

[gmx-users] Re: on MD at constant pH (Acoot Brett)

[Gerrit Groenhof]

You could have a look at 
Donnini et al, JCTC 7 (2011), 1962-1978
And with teh code available from 
http://www.mpibpc.mpg.de/home/grubmueller/projects/Methods/ConstpH/index.html
give it a try for your problem.

Gerrit

> 
>   1. on MD at constant pH (Acoot Brett)
>
> 
> Dear All,
> 
> Currently is it possible to run MD at a constant pH value?
> 
> I am looking forward to getting a reply from you.
> 
> Cheers,
> 
> Acoot
> -
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Re: [gmx-users] Re: How to add dihedral information from the GAFF topology

[bipin singh]

A lot of thanks to your "charitable mood" now the things has been resolved :) .
Thanks again.

On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul  wrote:
>
>
> bipin singh wrote:
>>
>> Thanks again
>>
>
> For the record, I didn't ask that you send me your files so I could
> troubleshoot for you.  Luckily for you I'm in a charitable mood this
> morning, so I took a look ;)
>
> Your problem is that you have a [molecules] directive in oct.itp.  Please
> refer to the documentation for the difference between a .top topology and a
> .itp topology:
>
> http://www.gromacs.org/Documentation/File_Formats/.itp_File
>
> The presence of this [molecules] directive tells grompp that the first thing
> it should expect is a block of octanol, when in fact your coordinate file
> has the protein first (starting with Ser-Leu, as I suspected).  You then
> have "1-octanol 1" in your topol.top, which says you're including another
> random octanol molecule somewhere later.
>
> You need a single [molecules] directive in the .top, which must match the
> order of the coordinate file.  Once you've got that, things should work
> fine.
>
> -Justin
>
>
>>> From the error It seems that I have placed the octane molecule before
>>
>> the protein but it is not the case, I dont know why grompp is reading
>> parameters for octane first and expecting it to match with protein. I
>> know that its my problem and I have to think about
>> that but just for the reference for you I am attaching the coordinate
>> and topology files.
>>
>> On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul  wrote:
>>>
>>>
>>> bipin singh wrote:

 Thanks for your inputs.

 I have checked the coordinate file thoroughly and the order of atoms
 are same as defined in the [molecules] directive.
 I really do not able to find out the source of the error.

>>> Looking closer at the error, what's happening is your octanol molecule is
>>> in
>>> a place where the topology expects the amino acid sequence Ser-Leu.
>>>  Perhaps
>>> that will help you track down the source of the problem.  It seems to me
>>> that your octanol molecule occurs earlier in the coordinate file than it
>>> does in the topology.
>>>
>>> If you still can't locate the problem, then you can always start over
>>> building your system in a known order, checking the alignment of the
>>> coordinate file and topology at every step.
>>>
>>> -Justin
>>>
>>>
 On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul  wrote:
>
>
> Biswajit Gorai wrote:
>>
>> Dear Bipin,
>> Edit your topology file as:
>>
>> ###
>> ; Include forcefield parameters
>> #include "amber99sb-ildn.ff/forcefield.itp"
>>
>> ; Include chain topologies
>> #include "topol_Protein_chain_A.itp"
>> #include "topol_Ion_chain_A2.itp"
>>
>> *#include "oct.itp"*
>>
> If oct.itp introduces new atom types (as the original .top does, for
> GAFF),
> placing this topology here will result in a fatal error since there is
> a
> new
> [atomtypes] directive that is introduced after the protein
> [moleculetype].
>  If oct.itp does not introduce any new atom types, its location within
> the
> system topology is irrelevant.
>
>> ; Include water topology
>> #include "amber99sb-ildn.ff/tip3p.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 "amber99sb-ildn.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> Ion_chain_A2        1
>> *1-octanol         1
>> *
>> *SOL              8987*
>
>
> Depending on the order of the coordinate file, it may not be possible
> to
> merge the SOL entries in this way.
>
> -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 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!
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> interface
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>>> --
>>> ==

Re: [gmx-users] Principal Components Analysis in Gromacs

[Thomas Evangelidis]

Hi Tsjerk,

Thanks for all the clarifications about PCA you make on the mailing list! I
have a question about the commandlines you wrote. Why do you use the .tpr
file with the "-s" flag? Is it because you want to compare the
mass-wheighted covariance matrices? I use to calculate the covariance
matrices by giving to g_covar a .pdb file with the "-s" flag and then
calculate the RMSIP without giving any structure file. I guess no masses
are used in that covariance analysis, right? Do you recommend using atom
masses for PCA in general?

Thanks in advance for any help.
Thomas



> - If you want to project the x-ray structures onto the eigenvectors
> from the MD simulations, you have to use
>
> g_anaeig -v eigenvec_from_md.trr -s reference.tpr -f xray_structures.pdb
> -proj
>
> - If you want to compare the similarity of the eigenvectors obtained
> from MD and from your crystal structures, you have to do PCA on both
> sets separately and then
>
> g_anaeig -v eigenvec_from_md.trr -v2 eigenvec_from_xray.trr -eig
> eigenval_from_md.xvg -eig2 eigenval_from_xray.xvg -s reference.tpr
> -inpr
>
>
>



-- 

==

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tev...@bioacademy.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [gmx-users] Where would I find the 45A4 GROMOS force field?

[Marc Gordon]

Ah well no worries. I will delve back into the gromacs and NAMD user guides
and see what I can dig up with regards to getting these GROMOS files
working through NAMD.

Thanks again for the help you have given me.

Marc


On Wed, Mar 28, 2012 at 4:19 PM, Justin A. Lemkul  wrote:

>
>
> Marc Gordon wrote:
>
>> Oh awesome. Thanks so much for this.
>>
>> I've never worked with GROMOS or gromacs themselves. I'm going to need to
>> look up whether or not it is possible to use these files to generate files
>> in the gromacs format required as input for NAMD now but at least having
>> access to the force fields puts me that much further along. I don't suppose
>> you know offhand whether such a thing is possible?
>>
>>
> Sorry, but I don't.  I haven't done anything with NAMD that wasn't out of
> the box.  That's probably a question better posed to the NAMD people.
>
> -Justin
>
>  I see they have a myriad of force fields available on ATB including the
>> other one I am interested in 53A6.
>>
>> Thanks again.
>>
>>
>> On Wed, Mar 28, 2012 at 2:50 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Marc Gordon wrote:
>>
>>Hi all
>>
>>I have never posted to the mailing list before but it has proven
>>very helpful in the past.
>>
>>I'm looking for the 45A4 force field. I've been asking Mr.
>>Google but so far I haven't had any luck locating it. This is I
>>imagine probably down to the wrong keywords or something
>>
>> I want to do some work on disaccharides and I would very much
>>like to use this force field. I'm going to be using it thorugh
>> NAMD.
>>
>>I thought this would be the best place to ask if anyone knew of
>>a site where this force field was being maintained or something.
>>
>>
>>You can get the files from ATB:
>>
>>http://compbio.biosci.uq.edu._**_au/atb/
>>
>>
>> 
>> >
>>
>>They are formatted for use with the GROMOS MD package, but that's
>>the only source of these files of which I'm aware.
>>
>>-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
>>
>>
>> 
>> >
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>>
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>>
>>
>> >
>> before posting!
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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] Position restraints problem

[Jernej Zidar]

True. Even more so if the position restraints file can be generated with basic 
Bash commands in under a minute.

Jernej

On 28. mar. 2012, at 20:16, gmx-users-requ...@gromacs.org wrote:

> It's pretty rare to have more than a handful of [moleculetype] sections, 
> each of which would want customized [position_restraints]. pdb2gmx will 
> write all-heavy-atom [position_restraints] sections which serve most 
> purposes. It would not be hard to modify genrestr to be useful in the 
> general case, but until a developer needs it badly enough, it'll be a 
> low priority :-)
> 
> Mark



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Re: [gmx-users] Principal Components Analysis in Gromacs

[Tsjerk Wassenaar]

Hi Thomas,

> Thanks for all the clarifications about PCA you make on the mailing list!

Thank you for the appreciation :)

> I have a question about the commandlines you wrote. Why do you use the .tpr
> file with the "-s" flag? Is it because you want to compare the
> mass-wheighted covariance matrices? I use to calculate the covariance
> matrices by giving to g_covar a .pdb file with the "-s" flag and then
> calculate the RMSIP without giving any structure file. I guess no masses are
> used in that covariance analysis, right? Do you recommend using atom masses
> for PCA in general?

Well, I admit that in most cases I don't use mass-weighting myself.
Unless you include hydrogens, it also doesn't matter much, as the
masses are not very different. Only if you want to calculate
frequencies, e.g. to connect to NMA and/or IR spectroscopy you would
really need masses.
If you use a .pdb or .gro file, you don't get mass-weighting. And
you're right that for calculating the RMSIP, and the subspace overlap,
and the martix of inner products, you don't need a structure filel,
but only the eigenvectors, and possibly the eigenvalues.

Cheers,

Tsjerk



-- 
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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[gmx-users] construction of homopolymer from non-standard monomers in gromacs

[Иимяа Фаамиилиияа]

Hi,

I am trying construct  homopolymer from non-standard  monomers .

I have pdb, itp and gro files for monomer and constructed pdb file for polymer. 
I can put them in corresponding  top/forcefield.ff directory.

But how I can get itp and gro files for polymer (for example, for 3-mer in 
simplest case)?

How Gromacs knows which atoms are "head" and "tail" atoms for connection of 
monomers 
into polymer (like in "Material Studio")?

Thank you in advance.
Igor




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[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

[Albert]

Dear:

  I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that the
efficiency for such simulation is only 3ns/day. I am wondering what
happen to my system or gromacs? What can I do to fasten the simulation?

here is my md.mdp:
*
title= god!
cpp  = /usr/bin/cpp
include  =
define   =
integrator   = md
dt   = 0.001
nsteps   = 1
nstxout  = 100
nstvout  = 100
nstlog   = 100
nstenergy= 1
nstxtcout= 10
xtc_grps =
energygrps = Protein POPC SOL ION
nstcalcenergy= 1
nstlist  = 1
nstcomm  = 1
comm_mode= Linear
comm-grps= Protein_POPCWater_and_ions
ns_type  = grid
rlist= 1.2
rlistlong = 1.4
vdwtype = Switch
rvdw = 1.2
rvdw_switch = 0.8
coulombtype  = pme
rcoulomb = 1.2
rcoulomb_switch = 0.0
fourierspacing = 0.15
pme_order = 4
DispCorr = no
tcoupl   = nose-hoover
nhchainlength= 1
tc-grps  = Protein_POPCWater_and_ions
tau_t= 0.50.5
ref_t= 310 310
Pcoupl   = parrinello-rahman
Pcoupltype   = semiisotropic
tau_p= 5.0
compressibility  = 4.5e-5   4.5e-5
ref_p= 1.0  1.0
pbc = xyz
gen_vel  = no
optimize_fft = no
constraints  = hbonds
constraint_algorithm = Lincs
*


Thank you very much

best
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Re: [gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

[Justin A. Lemkul]

Albert wrote:

Dear:

  I am using gromacs for membrane simulation (under CHARMM36 FF) which 
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster 
for such system with 2 fs time step. And what really astonished is that 
the efficiency for such simulation is only 3ns/day. I am wondering 
what happen to my system or gromacs? What can I do to fasten the simulation?




Use fewer processors.  You cannot necessarily assign a given system to an 
arbitrary number of processors and expect linear performance increase with the 
number of CPUs.  At some point, the communication overhead exceeds any speedup 
that might be obtained from using more CPUs.  For 80k atoms, I would try some 
benchmarks in the 64-96 CPU range to see how your performance is.  My rule of 
thumb is ~1000 atoms per CPU.  There are considerations for PP:PME node ratio 
when using DD, which also depend on the box type (see the Gromacs 4 paper and 
the manual for more details on such details).


-Justin


here is my md.mdp:
/
title= god!
cpp  = /usr/bin/cpp
include  =
define   =
integrator   = md
dt   = 0.001
nsteps   = 1
nstxout  = 100
nstvout  = 100
nstlog   = 100
nstenergy= 1
nstxtcout= 10
xtc_grps =
energygrps = Protein POPC SOL ION
nstcalcenergy= 1
nstlist  = 1
nstcomm  = 1
comm_mode= Linear
comm-grps= Protein_POPCWater_and_ions
ns_type  = grid
rlist= 1.2
rlistlong = 1.4
vdwtype = Switch
rvdw = 1.2
rvdw_switch = 0.8
coulombtype  = pme
rcoulomb = 1.2
rcoulomb_switch = 0.0
fourierspacing = 0.15
pme_order = 4
DispCorr = no
tcoupl   = nose-hoover
nhchainlength= 1
tc-grps  = Protein_POPCWater_and_ions
tau_t= 0.50.5
ref_t= 310 310
Pcoupl   = parrinello-rahman
Pcoupltype   = semiisotropic
tau_p= 5.0
compressibility  = 4.5e-5   4.5e-5
ref_p= 1.0  1.0
pbc = xyz
gen_vel  = no
optimize_fft = no
constraints  = hbonds
constraint_algorithm = Lincs 
/



Thank you very much

best



--


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] construction of homopolymer from non-standard monomers in gromacs

[Justin A. Lemkul]

Иимяа Фаамиилиияа wrote:

Hi,

I am trying construct  homopolymer from non-standard  monomers .

I have pdb, itp and gro files for monomer and constructed pdb file for polymer. 
I can put them in corresponding  top/forcefield.ff directory.


But how I can get itp and gro files for polymer (for example, for 3-mer in 
simplest case)?

How Gromacs knows which atoms are "head" and "tail" atoms for connection of monomers 
into polymer (like in "Material Studio")?




The best approach is to build .rtp entries and have pdb2gmx build your topology 
for you.  That way, you can build polymers of any size you like.  See the 
instructions and linked example at:


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

-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] 200 CPU, 3ns/day for 80,000 atoms !!!!

[Tsjerk Wassenaar]

Hi Albert,

You are doing neighboursearching every step! So every step all 200
CPUs need to know the how and what of all the other 199. Imagine the
communication overhead. Furthermore, you have 400 atoms per CPU
(neglecting the PME dedication). That will also make communication a
bottle neck. Which, incidentally, will show up when you finish or
terminate the run. According to the md.mdp you posted you're also
using a 1fs time step rather than 2fs.
Try decreasing the number of CPUs, and increasing nst*. Maybe you can
get much better performance if you have an 8- or 12-core around and
use a single machine. Certainly pays off if you need to do replicate
runs anyway.

Cheers,

Tsjerk

On Wed, Mar 28, 2012 at 5:31 PM, Albert  wrote:
> Dear:
>
>   I am using gromacs for membrane simulation (under CHARMM36 FF) which
> contains around 80,000 atoms. I've submitted over 200 CPU in the cluster for
> such system with 2 fs time step. And what really astonished is that the
> efficiency for such simulation is only 3ns/day. I am wondering what
> happen to my system or gromacs? What can I do to fasten the simulation?
>
> here is my md.mdp:
>
> title    = god!
> cpp  = /usr/bin/cpp
> include  =
> define   =
> integrator   = md
> dt   = 0.001
> nsteps   = 1
> nstxout  = 100
> nstvout  = 100
> nstlog   = 100
> nstenergy    = 1
> nstxtcout    = 10
> xtc_grps =
> energygrps         = Protein POPC SOL ION
> nstcalcenergy    = 1
> nstlist  = 1
> nstcomm  = 1
> comm_mode    = Linear
> comm-grps    = Protein_POPC    Water_and_ions
> ns_type  = grid
> rlist    = 1.2
> rlistlong         = 1.4
> vdwtype             = Switch
> rvdw = 1.2
> rvdw_switch         = 0.8
> coulombtype  = pme
> rcoulomb = 1.2
> rcoulomb_switch         = 0.0
> fourierspacing         = 0.15
> pme_order         = 4
> DispCorr             = no
> tcoupl   = nose-hoover
> nhchainlength    = 1
> tc-grps  = Protein_POPC    Water_and_ions
> tau_t    = 0.5        0.5
> ref_t    = 310         310
> Pcoupl   = parrinello-rahman
> Pcoupltype   = semiisotropic
> tau_p    = 5.0
> compressibility  = 4.5e-5   4.5e-5
> ref_p    = 1.0  1.0
> pbc             = xyz
> gen_vel  = no
> optimize_fft         = no
> constraints  = hbonds
> constraint_algorithm = Lincs
>
>
>
> Thank you very much
>
> best
>
> --
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-- 
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] 200 CPU, 3ns/day for 80,000 atoms !!!!

[Hannes Loeffler]

On Wed, 28 Mar 2012 17:31:47 +0200
Albert  wrote:

>   I am using gromacs for membrane simulation (under CHARMM36 FF) which
> contains around 80,000 atoms. I've submitted over 200 CPU in the
> cluster for such system with 2 fs time step. And what really
> astonished is that the efficiency for such simulation is only
> 3ns/day. I am wondering what happen to my system or gromacs? What
> can I do to fasten the simulation?

In addition to Justin's comment, you could also have a look into
our benchmark reports at
http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx to give you a
feeling for performance.

Cheers,
Hannes.
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Re: [gmx-users] Principal Components Analysis in Gromacs

[James Starlight]

Hi Tsjerk!

First, I'd like also thanks you for your  help.


Today I tried to make PCA of my X-ray data as well as comparison between
results of such PCA and EDA ( PCA wich is based on the MD trajectory of the
same protein).

In generaly I have no any problems with the X-ray PCA but I've forced with
some during comparison of results of both PCAs due to the different atom
numbers in both datasets ( X-ray structures consist of missing atoms ). As
I understood this problem could be solved by selection atoms for the MD
trajectory ( before PCA calculation of that data) wich are present in all
X-ray structures.

Because of the X-ray dataset consist of some missing residues in the loops
of structures I've had to reduce atom numbers in initial tpr topology.
So by means of tpbconv  I've made new .tpr file for this X-ray structures.
This new TPR was based on the  .tpr file wich I've obtained from the MD of
full-atomic model of protein. In new TPR I include only mainchain atoms as
well as residues presented in the X-ray structures ( I've defined it by
means of index.ndx file ). Does this aproach correct ? Are there any extra
ways to obtaint TPR file for my X-ray dataset  without redusing topology of
the MD structure ?

Also I'd like to ask some more about PCA results.

1) Firstly, what exactly is the new compresed trajectory made by
-filt filtered.xtc

In case of x-ray PCA this trajectory correspond to the initial numbers of
pdb's files but in case of MD_based PCA this trajectory consist of redused
number of atoms.

2) Also I'd like to know what actyally is the
-extr extremePCA.pdb ?

In case of MD_based PCA I've obtaned 20 different extreme.pdb trajectories
where 20 was the number of calculated Principal components.

But in case of X-ray PCA I've obtained only one such file wich was similar
to visualisation of the motion along softest PC althrough I've calculated
10 eigenvectors. Why in case of PCA I've obtain only one such file and what
exactly this trajectory is ? Is there any extra methods to visualise
motions along specified components ( not for ensembles of components )?

3) How I could specify exactly number of PC in the projection graphs ? AS I
understood 2d and 3d projections are made along the -first and -last
components. How I can make such projections based on two/ three another
specified components (e.g along 2 and 7 modes from 20 calculated) ?


Thanks for help,


James




28 марта 2012 г. 18:02 пользователь Tsjerk Wassenaar написал:

> Hi Thomas,
>
> > Thanks for all the clarifications about PCA you make on the mailing list!
>
> Thank you for the appreciation :)
>
> > I have a question about the commandlines you wrote. Why do you use the
> .tpr
> > file with the "-s" flag? Is it because you want to compare the
> > mass-wheighted covariance matrices? I use to calculate the covariance
> > matrices by giving to g_covar a .pdb file with the "-s" flag and then
> > calculate the RMSIP without giving any structure file. I guess no masses
> are
> > used in that covariance analysis, right? Do you recommend using atom
> masses
> > for PCA in general?
>
> Well, I admit that in most cases I don't use mass-weighting myself.
> Unless you include hydrogens, it also doesn't matter much, as the
> masses are not very different. Only if you want to calculate
> frequencies, e.g. to connect to NMA and/or IR spectroscopy you would
> really need masses.
> If you use a .pdb or .gro file, you don't get mass-weighting. And
> you're right that for calculating the RMSIP, and the subspace overlap,
> and the martix of inner products, you don't need a structure filel,
> but only the eigenvectors, and possibly the eigenvalues.
>
> Cheers,
>
> Tsjerk
>
>
>
> --
> 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] Where would I find the 45A4 GROMOS force field?

[Oliver Stueker]

Hi Marc,

Though I never came across ready-to-use files for Gromos 45A4, you can
for sure get all the parameters for carbohydrates from [1] and
transfer them into a Gromacs format (make sure to convert all the
units).

Searching briefly for the term 45A4 in [2] lets me believe, that the
parameters have been cooperated into 53A5 and 53A6, so you might want
to check that as well.

[1] Lins RD, Hunenberger PH (2005)
A new GROMOS force field for hexopyranose-based carbohydrates.
Journal of Computational Chemistry 26: 1400-1412.
Available: http://dx.doi.org/10.1002/jcc.20275.
[2] Oostenbrink C, Villa A, Mark AE, Gunsteren WF van (2004)
A biomolecular force field based on the free enthalpy of hydration
and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.
Journal of Computational Chemistry 25: 1656-76.
Available: http://dx.doi.org/10.1002/jcc.20090.

Oliver

On Wed, Mar 28, 2012 at 07:28, Marc Gordon  wrote:
> Ah well no worries. I will delve back into the gromacs and NAMD user guides
> and see what I can dig up with regards to getting these GROMOS files working
> through NAMD.
>
> Thanks again for the help you have given me.
>
> Marc
>
>
>
> On Wed, Mar 28, 2012 at 4:19 PM, Justin A. Lemkul  wrote:
>>
>>
>>
>> Marc Gordon wrote:
>>>
>>> Oh awesome. Thanks so much for this.
>>>
>>> I've never worked with GROMOS or gromacs themselves. I'm going to need to
>>> look up whether or not it is possible to use these files to generate files
>>> in the gromacs format required as input for NAMD now but at least having
>>> access to the force fields puts me that much further along. I don't suppose
>>> you know offhand whether such a thing is possible?
>>>
>>
>> Sorry, but I don't.  I haven't done anything with NAMD that wasn't out of
>> the box.  That's probably a question better posed to the NAMD people.
>>
>> -Justin
>>
>>> I see they have a myriad of force fields available on ATB including the
>>> other one I am interested in 53A6.
>>>
>>> Thanks again.
>>>
>>>
>>> On Wed, Mar 28, 2012 at 2:50 PM, Justin A. Lemkul >> > wrote:
>>>
>>>
>>>
>>>    Marc Gordon wrote:
>>>
>>>        Hi all
>>>
>>>        I have never posted to the mailing list before but it has proven
>>>        very helpful in the past.
>>>
>>>        I'm looking for the 45A4 force field. I've been asking Mr.
>>>        Google but so far I haven't had any luck locating it. This is I
>>>        imagine probably down to the wrong keywords or something
>>>
>>>         I want to do some work on disaccharides and I would very much
>>>        like to use this force field. I'm going to be using it thorugh
>>> NAMD.
>>>
>>>        I thought this would be the best place to ask if anyone knew of
>>>        a site where this force field was being maintained or something.
>>>
>>>
>>>    You can get the files from ATB:
>>>
>>>    http://compbio.biosci.uq.edu.__au/atb/
>>>
>>>    
>>>
>>>    They are formatted for use with the GROMOS MD package, but that's
>>>    the only source of these files of which I'm aware.
>>>
>>>    -Justin
>>>
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Re: [gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark,


thanks for explanation again.


28 марта 2012 г. 16:04 пользователь Mark Abraham
написал:

 That can mean big restraint forces and tiny integration steps and lots of
> tweaking and praying.
>

Yes I think this aproach could be usefull in my case. Actually I want to
move some parts of the helices of my protein in the deired direction up to
6-10 A. There is the data showing that this new conformation is very
unstabile and short-lived in the absense of some additional external
factors. But also I've seen that application of big restrained forces
perturbed the overal structure of my protein considerably. So the good
sollution might be application of such forces  with the position restraines
simultaneously. What do you think about the most trivial aproach: e.g if I
could not applied posres on the desired atoms and use default posres
generated by pdb2gmx on the all atoms. At the same time I'm using more
strongest distance restrains on the desired positions to move this atoms
even the precense of weaker posres applied on this. Finally because posres
act on the others atoms I can prevent destabilisation of the whole protein.
Might this aproach be usefull? And what difference between forses of the
posres ( 1000 kj) and disres must be to generate expected effect ?


James

>
>
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[gmx-users] x,y and z components of rmsf?

[patrick wintrode]

Does some one know of a way to get g_rms or g_rmsf to write out the x, y, and z 
components of the rms(f) for each atom/residue separately?

Thanks.

Patrick L. Wintrode
Department of Pharmaceutical Sciences
University of Maryland
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Re: [gmx-users] x,y and z components of rmsf?

[Erik Marklund]

I believe that rmsf can compute anisotropic b-factors, but have not tried it 
myself.

Erik


28 mar 2012 kl. 22.32 skrev patrick wintrode:

> Does some one know of a way to get g_rms or g_rmsf to write out the x, y, and 
> z components of the rms(f) for each atom/residue separately?
> 
> Thanks.
> 
> Patrick L. Wintrode
> Department of Pharmaceutical Sciences
> University of Maryland
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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Re: [gmx-users] Generation of the Distance Restraints

[Mark Abraham]

On 29/03/2012 5:53 AM, James Starlight wrote:

Mark,


thanks for explanation again.


28 ? 2012 ?. 16:04  Mark Abraham 
mailto:mark.abra...@anu.edu.au>> ???:


 That can mean big restraint forces and tiny integration steps and
lots of tweaking and praying.


Yes I think this aproach could be usefull in my case. Actually I want 
to move some parts of the helices of my protein in the deired 
direction up to 6-10 A. There is the data showing that this new 
conformation is very unstabile and short-lived in the absense of some 
additional external factors. But also I've seen that application of 
big restrained forces perturbed the overal structure of my protein 
considerably. So the good sollution might be application of such 
forces  with the position restraines simultaneously. What do you think 
about the most trivial aproach: e.g if I could not applied posres on 
the desired atoms and use default posres generated by pdb2gmx on the 
all atoms. At the same time I'm using more strongest distance 
restrains on the desired positions to move this atoms even the 
precense of weaker posres applied on this. Finally because posres act 
on the others atoms I can prevent destabilisation of the whole 
protein. Might this aproach be usefull? And what difference between 
forses of the posres ( 1000 kj) and disres must be to generate 
expected effect ?


Yeah, some kind of hybrid treatment of distance and position restraints 
could be required. I've no idea on required force constants - this kind 
of thing (breaking the force field to set up initial conditions that you 
expect are fairly unphysical) is very situation dependent. Nobody really 
does it often enough for there to be a general body of knowledge.


Mark
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RE: [gmx-users] x,y and z components of rmsf?

[Asaf Farhi]

Dear GMCS users

Hi. Does anyone know if MD at 2K is feasible?

Thanks,
Best regards,
Asaf

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Erik Marklund [er...@xray.bmc.uu.se]
Sent: Wednesday, March 28, 2012 10:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] x,y and z components of rmsf?

I believe that rmsf can compute anisotropic b-factors, but have not tried it 
myself.

Erik


28 mar 2012 kl. 22.32 skrev patrick wintrode:

Does some one know of a way to get g_rms or g_rmsf to write out the x, y, and z 
components of the rms(f) for each atom/residue separately?

Thanks.

Patrick L. Wintrode
Department of Pharmaceutical Sciences
University of Maryland

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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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[gmx-users] crazy temperatures

[Mark Abraham]

On 29/03/2012 9:39 AM, Asaf Farhi wrote:

Dear GMCS users

Hi. Does anyone know if MD at 2K is feasible?



Please start new email threads rather than hijacking old ones.

I doubt anybody knows the answer to your question. Force fields are 
parameterized to reproduce data at around 300K. I can't imagine any 
possible use for simulating an MM force field at a temperature hotter 
than the sun.


Mark
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Re: [gmx-users] crazy temperatures

[Warren Gallin]

At that temperature most matter is going to be a plasma, not many bonds to be 
simulated and a lot of free electrons.

Warren Gallin

On 2012-03-28, at 4:43 PM, Mark Abraham wrote:

> On 29/03/2012 9:39 AM, Asaf Farhi wrote:
>> Dear GMCS users
>> 
>> Hi. Does anyone know if MD at 2K is feasible?
>> 
> 
> Please start new email threads rather than hijacking old ones.
> 
> I doubt anybody knows the answer to your question. Force fields are 
> parameterized to reproduce data at around 300K. I can't imagine any possible 
> use for simulating an MM force field at a temperature hotter than the sun.
> 
> Mark
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[gmx-users] Re:200 CPU, 3ns/day for 80,000 atoms

[Dr. Vitaly V. Chaban]

>  I am using gromacs for membrane simulation (under CHARMM36 FF) which
> contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
> for such system with 2 fs time step. And what really astonished is that the
> efficiency for such simulation is only 3ns/day. I am wondering what
> happen to my system or gromacs? What can I do to fasten the simulation?
>
> here is my md.mdp:
> *
> title                    = god!
> cpp                      = /usr/bin/cpp
> include                  =
> define                   =
> integrator               = md
> dt                       = 0.001
> nsteps                   = 1
> nstxout                  = 100
> nstvout                  = 100
> nstlog                   = 100
> nstenergy                = 1
> nstxtcout                = 10
> xtc_grps                 =
> energygrps         = Protein POPC SOL ION
> nstcalcenergy            = 1
> nstlist                  = 1
> nstcomm                  = 1
> comm_mode                = Linear
> comm-grps                = Protein_POPC    Water_and_ions
> ns_type                  = grid
> rlist                    = 1.2
> rlistlong         = 1.4
> vdwtype             = Switch
> rvdw                     = 1.2
> rvdw_switch         = 0.8
> coulombtype              = pme
> rcoulomb                 = 1.2
> rcoulomb_switch         = 0.0
> fourierspacing         = 0.15
> pme_order         = 4
> DispCorr             = no
> tcoupl                   = nose-hoover
> nhchainlength            = 1
> tc-grps                  = Protein_POPC    Water_and_ions
> tau_t                    = 0.5            0.5
> ref_t                    = 310         310
> Pcoupl                   = parrinello-rahman
> Pcoupltype               = semiisotropic
> tau_p                    = 5.0
> compressibility          = 4.5e-5       4.5e-5
> ref_p                    = 1.0          1.0
> pbc             = xyz
> gen_vel                  = no
> optimize_fft         = no
> constraints              = hbonds
> constraint_algorithm     = Lincs
> *


This discussion should be started with you reporting the speedup for
your system with 200cpu's. Rather than appealing just to some velocity
per nanosecond.

Neighborsearching is inefficient. Outputting immediate velocities
every 100 steps is senseless.


Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] using MPI

[cuong nguyen]

Thanks Erik,
In case I run my simulations on 4 nodes, please let me know what do I have
to add to the command to start "MPI"? I have used the commands:
*grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top
mdrun -s NVT_50ns -o NVT_50ns -c NVT_50ns -x NVT_50ns -e NVT_50ns -g
NVT_50ns -v*
however, the speed was still the same.
Best regards,

Cuong

2012/3/15 Erik Marklund 

> If you are to run on a single node, then there's no need for mpi nowadays.
> mdrun uses all cores it can find anyway. If you need to split your
> calculation over many machines, however, you will need mpi.
>
> Best,
>
> Erik
>
> 15 mar 2012 kl. 04.50 skrev cuong nguyen:
>
> Dear Gromacs users,
>
> I prepare to run my simulations on the supercomputer on single node with
> 64 CPUs. Although I have seen on Gromacs Mannual suggesting to use MPI to
> parellel, I still haven't understood how to use this application and which
> commands I have to use. Please help me to deal with this?
>
> Many thanks and regards,
>
> Cuong
>
>
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>
> ---
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> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 6688fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
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Mobile: (+61) 452213981
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[gmx-users] Calculate Bulk Pressure Tensor?

[Weilong Zhao]

Hi,

I was trying to calculate the pressure tensors for one of my solid crystal
systems. I notice that g_energy does have this option---pressure xx,
pressure yy and pressure zz, however the results seem to be a function of
running time. How can I extract information about pressure tensor at
different position of my solid system? If gromacs allows me to do so, do I
need to integrate the tensor value from one position to another position?
Thanks very much for reading! Your kind help is greatly appreciated.

-- 
Weilong Zhao
Graduate Student
Department of Polymer Science
University of Akron
Akron, OH 44325
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[gmx-users] Re: crazy temperatures

[Dr. Vitaly V. Chaban]

> Dear GMCS users
>
> Hi. Does anyone know if MD at 2K is feasible?

Aggregate state, not temperature, matters if you want to discuss
potential models applicability.

I believe at ~10,000K one can get quite realistic results for the
gaseous phase of certain high-melting substances like CaO or MgS.


Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] using MPI

[Mark Abraham]

On 29/03/2012 12:25 PM, cuong nguyen wrote:

Thanks Erik,
In case I run my simulations on 4 nodes, please let me know what do I 
have to add to the command to start "MPI"? I have used the commands:

/grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top
mdrun -s NVT_50ns -o NVT_50ns -c NVT_50ns -x NVT_50ns -e NVT_50ns -g 
NVT_50ns -v/

however, the speed was still the same.


You need to find out what MPI you have installed and consult the 
available documentation for that. We cannot help you with that.


Mark


Best regards,

Cuong

2012/3/15 Erik Marklund >


If you are to run on a single node, then there's no need for mpi
nowadays. mdrun uses all cores it can find anyway. If you need to
split your calculation over many machines, however, you will need
mpi.

Best,

Erik

15 mar 2012 kl. 04.50 skrev cuong nguyen:


Dear Gromacs users,
I prepare to run my simulations on the supercomputer on single
node with 64 CPUs. Although I have seen on Gromacs Mannual
suggesting to use MPI to parellel, I still haven't understood how
to use this application and which commands I have to use. Please
help me to deal with this?
Many thanks and regards,
Cuong

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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone: +46 18 471 6688 fax:
+46 18 511 755 
er...@xray.bmc.uu.se 
http://www2.icm.uu.se/molbio/elflab/index.html


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--
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981





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[gmx-users] crazy temperatures

[chris . neale]

I disagree.

What one is generally trying to obtain with elevated temperatures is  
enhanced sampling, not temperature-dependent properties. I believe  
that even TIP4P-EW is not very good at getting the properties of water  
correct at 600 K, temperatures that are commonly used during replica  
exchange simulations (not to mention that nobody has any idea how  
accurate protein forcefields are at temperatures other than the one at  
which they were parameterized).


So I think that doing simulations at massively elevated temperatures  
can possibly be useful.


That said, while doing simulated annealing, I have found previously  
using charmm that once you get to about 3,000 K you will get chiral  
inversions that can not resolve at lower temperature. This is because  
our improper dihedral terms only maintain the given chirality, rather  
than favouring one over the other.


To address your question directly, I believe that chiral inversions  
will be a big problem for you at 20,000 K. Obviously you also have  
simulation stability issues, but one presumes that you could resolve  
those by using a small enough timestep.


Chris.

-- original message --

At that temperature most matter is going to be a plasma, not many  
bonds to be simulated and a lot of free electrons.


Warren Gallin

On 2012-03-28, at 4:43 PM, Mark Abraham wrote:

[Hide Quoted Text]
On 29/03/2012 9:39 AM, Asaf Farhi wrote:
Dear GMCS users

Hi. Does anyone know if MD at 2K is feasible?
Please start new email threads rather than hijacking old ones.

I doubt anybody knows the answer to your question. Force fields are  
parameterized to reproduce data at around 300K. I can't imagine any  
possible use for simulating an MM force field at a temperature hotter  
than the sun.


Mark
--


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Re: [gmx-users] Re:200 CPU, 3ns/day for 80,000 atoms

[Mark Abraham]

On 29/03/2012 11:03 AM, Dr. Vitaly V. Chaban wrote:

  I am using gromacs for membrane simulation (under CHARMM36 FF) which
contains around 80,000 atoms. I've submitted over 200 CPU in the cluster
for such system with 2 fs time step. And what really astonished is that the
efficiency for such simulation is only 3ns/day. I am wondering what
happen to my system or gromacs? What can I do to fasten the simulation?

here is my md.mdp:
*
title= god!
cpp  = /usr/bin/cpp
include  =
define   =
integrator   = md
dt   = 0.001
nsteps   = 1
nstxout  = 100
nstvout  = 100
nstlog   = 100
nstenergy= 1
nstxtcout= 10
xtc_grps =
energygrps = Protein POPC SOL ION
nstcalcenergy= 1


I agree with the other thoughts mentioned, and would add that 
nstcalcenergy = 1 triggers global communication every integration step, 
and that is increasingly inefficient at high parallelization.


Mark
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Re: [gmx-users] x,y and z components of rmsf?

[Tsjerk Wassenaar]

Please start a new thread for a new topic.

T.

On Thu, Mar 29, 2012 at 12:39 AM, Asaf Farhi wrote:

>  Dear GMCS users
>
>  Hi. Does anyone know if MD at 2K is feasible?
>
>  Thanks,
> Best regards,
> Asaf
>  --
> *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Erik Marklund [er...@xray.bmc.uu.se]
> *Sent:* Wednesday, March 28, 2012 10:37 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] x,y and z components of rmsf?
>
>  I believe that rmsf can compute anisotropic b-factors, but have not
> tried it myself.
>
>  Erik
>
>
>  28 mar 2012 kl. 22.32 skrev patrick wintrode:
>
>   Does some one know of a way to get g_rms or g_rmsf to write out the x,
> y, and z components of the rms(f) for each atom/residue separately?
>
> Thanks.
>
> Patrick L. Wintrode
> Department of Pharmaceutical Sciences
> University of Maryland
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>
>   ---
> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 6688fax: +46 18 511 755
> er...@xray.bmc.uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
>
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-- 
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] x,y and z components of rmsf?

[Tsjerk Wassenaar]

Hi Patrick,

You can extract the diagonal from the covariance matrix generated with
g_covar (-ascii). That is equal to the RMSF per atom-coordinate.

Cheers,

Tsjerk

On Wed, Mar 28, 2012 at 10:32 PM, patrick wintrode wrote:

> Does some one know of a way to get g_rms or g_rmsf to write out the x, y,
> and z components of the rms(f) for each atom/residue separately?
>
> Thanks.
>
> Patrick L. Wintrode
> Department of Pharmaceutical Sciences
> University of Maryland
>
> --
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-- 
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] Re: crazy temperatures

[Tsjerk Wassenaar]

Hey,

Hotter than the sun only goes for the surface. The core and the corona
are much hotter. Whether electrons get separated from nuclei or
nuclear fusion should start to occur also depends on pressure... But
the question itself pertains to the code and the application of
Newton's equations of motion for particle based systems at very high
temperatures. And there's nothing that should prohibit that. There are
practical issues, of course. The state of the matter you intend to
simulate, the force field, and the time step, definitely.

Cheers,

Tsjerk

On Thu, Mar 29, 2012 at 4:11 AM, Dr. Vitaly V. Chaban
 wrote:
>> Dear GMCS users
>>
>> Hi. Does anyone know if MD at 2K is feasible?
>
> Aggregate state, not temperature, matters if you want to discuss
> potential models applicability.
>
> I believe at ~10,000K one can get quite realistic results for the
> gaseous phase of certain high-melting substances like CaO or MgS.
>
>
> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
> Univ. Rochester, Rochester, New York 14627-0216
> THE UNITED STATES OF AMERICA
> --
> gmx-users mailing list    gmx-users@gromacs.org
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-- 
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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[gmx-users] About movie in GROMACS

[rama david]

HI Gromacs Friends,
 I complete one simulation for 4 different molecule  placed
apart
in box of  dimension 4 4 4 ..
when I used the trajectory I saw the one molecule interact with each other
but they are
getting broken because of box..(Some part protruding from other side).
To see movie I used the command
1. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc nojump -dt 10
 The molecules moving apart without any interaction

2. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc whole -dt 10
 The molecules are interacting in cell ..
  but because of periodic cell , near the cell boundary  the molecule
 interaction get remove and molecules come in cell from other side..
( I know it is because of periodic boundary condition ..one goes from
right
  hand side come in cell through left hand side )

To see the four molecule interacting each other near also cell boundary ,
what command
I have to use ???
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[gmx-users] non-equilibrium MD

[Acoot Brett]

Dear All,

What will be the difference for run regular production MD and non-equilibrium 
MD? And website introduction?

Cheers,

Acoot-- 
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[gmx-users] Shima Arasteh wants to share a link | Gromacs

[ros...@kth.se]

Shima Arasteh wants to a share a link on the Gromacs wiki: 
http://www.gromacs.org/

Shima Arasteh says:
Dear Gromacs friends,
I am a new user of Gromacs, following the kalp-15 in DPPC tutorial instruction 
but I face a fatal error when I enter this command:
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

And the fatal error is this:
atomtype LC3 not found

Anybody can suggest me a solution to solve my problem?

Thanks in advance
Shima
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[gmx-users] Pressure coupling doubt

[bipin singh]

Hello,

I have two doubts regarding pressure coupling in Gromacs:

1) When I use pcoupl=no

the mdp.out shows the following

; Pressure coupling
pcoupl   = no
Pcoupltype   = Isotropic
nstpcouple   = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 1
compressibility  =
ref-p=

I have not used the pcoupl(=no) then why it is showing Pcoupltype=Isotropic.


(2) This is a silly question: What will happen if we use following
option in mdp of NVT simulation:

 pcoupl=no
 compressibility= 4.5e-5

does it will affect the NVT criteria ? or It will ignore the
compressibility input?
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AW: [gmx-users] About movie in GROMACS

[Rausch, Felix]

Hi.

Take a look at the "-center" flag of trjconv. Together with "-pbc" (and maybe 
also "-ur") it should be possible to center your molecules of interest in the 
middle of the simulation cell.


Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im 
Auftrag von rama david
Gesendet: Donnerstag, 29. März 2012 07:18
An: Discussion list for GROMACS users
Betreff: [gmx-users] About movie in GROMACS

HI Gromacs Friends,
 I complete one simulation for 4 different molecule  placed apart
in box of  dimension 4 4 4 ..
when I used the trajectory I saw the one molecule interact with each other but 
they are
getting broken because of box..(Some part protruding from other side).
To see movie I used the command
1. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc nojump -dt 10
 The molecules moving apart without any interaction

2. trjconv -s ..tpr  -f ..xtc  -o movie.pdb -pbc whole -dt 10
 The molecules are interacting in cell ..
  but because of periodic cell , near the cell boundary  the molecule
 interaction get remove and molecules come in cell from other side..
( I know it is because of periodic boundary condition ..one goes from right
  hand side come in cell through left hand side )

To see the four molecule interacting each other near also cell boundary , what 
command
I have to use ???
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