Re: [gmx-users] Thermostating in NEMD

[David van der Spoel]

On 2010-11-27 23.54, Apoorv Kalyankar wrote:

Hi,

I was wondering how does a thermostat work in a Non Equilibrium
Simulation(NEMD) in GROMACS.
Does it subtract out the streaming velocity before applying the
thermostat or does it not apply thermostat at all in
the direction of the applied acceleration?
Thanks.

check source code in src/mdlib/update.c
IIRC it does not scale the group velocities resulting from acceleration 
and hence only the internal temperature is scaled.




Apoorv Kalyankar
Graduate Student
Mechanical Science and Engineering
Unviersity of Illinois at Urbana-Champaign




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[gmx-users] fix center of mass vs fix residues close to COM

[哦哦]

dear all,
  I  am doing a simluation that I want to fix the center of mass of  
three protein chains , so that they don`t move to much away , should I fix 
center of mass of every chains, or fix residues that most close to COM. what is 
the diffenerces between the two method? and if I want to fix center of mass, 
what should I do?  change comm_grps= chain_a  chain_b chain_c SOL , comm_mode   
=  Angular ?  should I change other places?
 
best wishes~
yuanyuan-- 
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Re: [gmx-users] Replica exchange

[Mark Abraham]

On 28/11/2010 4:49 AM, Sai Pooja wrote:

Hi,
I am running a script that uses mdrun of gromacs and does replica 
exchange (not using -replex). The reason is that I want to use 
different table files for different replicas. However, it seems that I 
cannot supply unique table names. For example, if I supply a table 
name different from table_Protein_SOL.xvg for protein solvent 
interactions, like rex0_table_Protein_SOL.xvg, I get an error -
Yeah, the multi-simulation internal filename-suffixing mechanism doesn't 
apply to table files like it does to various of the other files. I think 
such suffixing would be a feature that should be incorporated, and so I 
encourage you to file a feature request in the Bugzilla system. Perhaps 
there are other file types in this category.

Fatal error:
Library file in current dir nor  not found table_Protein_SOL.xvgin 
default directories.


If you update GROMACS, this garbled error message is fixed.

Mark


(You can set the directories to search with the GMXLIB path variable)
For more information and tips for troubleshooting, please check the 
GROMACS

To oversome this limitation, I am using something like this:
[pseudocode]
for r 1 to n:
   copy rex_r_Protein_SOL.xvg table_Protein_SOL.xvg
   mdrun -s .. -table table.xvg -table table_Protein_SOL.xvg ...
Will mdrun be able to run with separate table parameters in this way?
Pooja

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[gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)

[Jignesh Patel]

Dear Justin,

Thanks for your reply.
I have checked whole pdb file. Everything is fine.

When I remove phosphorylated serine and use only serine then every thing
went fine.

co-ordinates for phosphoserine are as per following

ATOM   1684  N   SEP X 167  27.040  22.580   8.280  1.00
0.00
ATOM   1685  H   SEP X 167  27.150  23.470   7.820  1.00
0.00
ATOM   1686  CA  SEP X 167  28.020  22.270   9.340  1.00
0.00
ATOM   1687  CB  SEP X 167  29.330  21.760   8.740  1.00
0.00
ATOM   1688  OG  SEP X 167  30.210  21.300   9.770  1.00
0.00
ATOM   1689  P   SEP X 167  29.763  21.418  10.657  0.80  0.00
ATOM   1690  O1P SEP X 167  30.228  20.602  11.000  0.80
0.00
ATOM   1691  O2P SEP X 167  29.298  22.234  10.314  0.80
0.00
ATOM   1692  O3P SEP X 167  29.316  21.536  11.544  0.80  0.00
ATOM   1693  C   SEP X 167  28.320  23.540  10.140  1.00
0.00
ATOM   1694  O   SEP X 167  28.980  24.460   9.660  1.00  0.00

and following details regarding the error,

Identified residue MET1 as a starting terminus.
Warning: Residue SEP167 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ASN168 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue PHE169 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ALA170 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue VAL171 in chain has different type (Protein) from starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue GLN166 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1  HIS122  CYS127  MET155  HIS181  CYS232
 SD5  NE2953   SG987  SD1198 NE21417  SG1802
  HIS122  NE2953   0.896
  CYS127   SG987   2.406   2.338
  MET155  SD1198   2.631   2.424   0.726
  HIS181 NE21417   2.143   2.161   2.124   1.774
  CYS232  SG1802   2.805   3.428   3.766   3.748   2.309
  HIS273 NE22097   4.614   4.982   4.609   4.323   3.017   2.266
Start terminus: NH3+
End terminus: COO-
Checking for duplicate atoms
Now there are 283 residues with 2821 atoms
Making bonds...
Number of bonds was 2866, now 2861
Generating angles, dihedrals and pairs...
Before cleaning: 4579 pairs

---
Program pdb2gmx_d, VERSION 4.5.1
Source code file: pgutil.c, line: 88

Fatal error:
Atom N not found in residue seq.nr. 1 while adding improper

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Thanking you.

With regards,
Jignesh Patel



On Sat, Nov 27, 2010 at 4:30 PM, gmx-users-requ...@gromacs.org wrote:

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 Today's Topics:

   1. Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)
   2. Re: Free Energy Calculation: dVpot/dlambda is always zero
  (Anirban Ghosh)


 --

 Message: 1
 Date: Fri, 26 Nov 2010 22:48:22 -0500
 From: Justin A. Lemkul jalem...@vt.edu
 Subject: Re: [gmx-users] Error while using forcefield GROMOS 43a1p
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 4cf07f86.8030...@vt.edu
 Content-Type: text/plain; charset=ISO-8859-1; format=flowed



 Jignesh Patel wrote:
  Dear Justin,
 
  I am trying to do simulation of a system which contains phosphorylated
  serine using  GROMOS 43a1p forcefield. While running pdb2gmx command, I
  am getting following error.
  Fatal error:
  Atom N not found in residue seq.nr http://seq.nr. 1 while adding
 improper
 

 Well, either the N atom of residue 1 is not present in your .pdb file (in
 which
 case you've got a broken structure that needs fixing), or something else is
 going on.  Without seeing the contents of your input coordinate file (just
 the
 first residue, really) and your pdb2gmx command line, there's not much help
 anyone can give you.

 -Justin

  thank you in anticipation.
 
  With regards,
  Jignesh Patel
 

 --
 

 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