[gmx-users] Re FTP server down

[Dallas B. Warren]

Sorry seems that it was just me, or it is back up. Either way things  
are good now.


Catch ya,
Dallas Warren

A polar bear is a rectangular bear that has undergone a polar  
transformation

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] ftp Server Down?

[Dallas B. Warren]

Is it just me, or is it down at the moment? Trying to get the latest  
version source files.


Catch ya,
Dallas Warren

A polar bear is a rectangular bear that has undergone a polar  
transformation

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] About frozen groups

[Justin A. Lemkul]

Mohammed Kamal wrote:
 
Many thanks for Justin for your helpful comments, I think I still need 
your help for the first question... I have included more details about 
my system below
 
 
 
 > Mohammed Kamal wrote:

 >
 > > Tcoupl = berendsen
 > >
 > > tau_t = 0.1 0.1 0.1 0.1
 > >
 > > tc_grps = protein T27 SOL Cl ; T27 is the ligand
 >
 > General advice: do not couple solvent and ions separately. I believe 
there is a

 > newer version of the tutorial that fixes this information. See here:
 >
 > http://wiki.gromacs.org/index.php/thermostats
 
Thanks much for that advice




Another thing that I just noticed as I scrolled through.  "Cl" corresponds to a 
chloride ion under ffgmx.  This force field is long since deprecated, and should 
not be used for new simulations.  Go with a newer Gromos96 force field.



 >
 > >
 > > ref_t = 300 300 300 300
 > >
 > > *energygrps = protein T27 SOL *
 > >
 > > *energygrp_excl = IRS IRS IRS SOL*
 > >
 > > *freezegrps = IRS*
 > >
 > > *freezedim = Y Y Y*
 > >
 > > Pcoupl = berendsen
 > >
 > > pcoupltype = isotropic
 > >
 > > tau_p = 0.5
 > >
 > > compressibility = 4.5e-5
 > >
 > > ref_p = 1.0
 > >
 > > gen_vel = yes
 > >
 > > gen_temp = 300
 > >
 > > gen_seed = 173529
 > >
 > >
 > >
 > > and when I used the grommp line of
 > >
 > > *grompp* -f md.mdp -c 2zd1_eq.gro -p 2zd1.top -n IRS.ndx -o md.tpr
 > >
 > > I had (as expected) an error massage states that IRS is not an energy
 > > group however if I have added IRS as an energy group I had an error 
that

 > > some atoms are in multiple energy Mon. groups.
 > >
 >
 > Well, what is IRS? Is it a protein, another molecule? You've got very
 > different groups labeled for energy monitoring and energygrp-excl, so 
something
 > needs to be fixed. Without any clue what exactly you're dealing with, 
it's hard

 > to give any useful information.
 >
 
 

IRS is a group of residues in the protein, suppose that my protein has 
50 residues, IRS is a group that contains residues 2, 7, 9, 15, 45 for 
example. So the IRS group is actually part of my protein


Now I have four groups the SOL, ligand (T27), protein and IRS which 
overlapped with the protein (this is the problem) ...


I need to fix the position of IRS residues and exclude the non-bonding 
interactions between these residues and the solvent. Gromacs will not 
accept IRS as an energy group because there will be some residues that 
are common with the protein and so I can't state it in the energy 
exclusions??


 


No, since IRS and your Protein have common (bonded) interactions, you cannot 
simply specify an exclusion to separate IRS from the protein.


The following is just thinking out loud, others please feel free to comment 
since I have never tried anything like this: It may be possible to specify a 
modified "Protein" index group that contains all residues NOT including your IRS 
residues (type "help" at the make_ndx prompt to see examples of clever syntax). 
 These groups could be merged for the purpose of T-coupling (i.e., 
Protein_IRS), but then specified differently for energygrps and energygrp_excl.


Worth a shot, but as I said, I've never done anything like that.



That's fine... so if I just add unconditional #include "POSRE_IRS.itp" 
to the .top file Gromacs will apply postion restraints even without 
adding the define line to the .mdp file?


Correct, just be careful that artificial restraints do not influence the 
dynamics of interest.


-Justin

--


Justin A. Lemkul
Graduate Research Assistant
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] About frozen groups

[Mohammed Kamal]

 
Many thanks for Justin for your helpful comments, I think I still need your 
help for the first question... I have included more details about my system 
below
 
 
 
> Mohammed Kamal wrote:> > > Tcoupl = berendsen> > > > tau_t = 0.1 0.1 0.1 0.1> 
> > > > tc_grps = protein T27 SOL Cl ; T27 is the ligand> > General advice: do 
> not couple solvent and ions separately. I believe there is a > newer version 
> of the tutorial that fixes this information. See here:> > 
> http://wiki.gromacs.org/index.php/thermostats
 
Thanks much for that advice
> > > > > ref_t = 300 300 300 300> > > > *energygrps = protein T27 SOL *> > > > 
> > > > > *energygrp_excl = IRS IRS IRS SOL*> > > > *freezegrps = IRS*> > > > 
> > > > > *freezedim = Y Y Y*> > > > Pcoupl = berendsen> > > > pcoupltype = 
> > > > > isotropic> > > > tau_p = 0.5> > > > compressibility = 4.5e-5> > > > 
> > > > > ref_p = 1.0> > > > gen_vel = yes> > > > gen_temp = 300> > > > 
> > > > > gen_seed = 173529> > > > > > > > and when I used the grommp line of> 
> > > > > > > > *grompp* -f md.mdp -c 2zd1_eq.gro -p 2zd1.top -n IRS.ndx -o 
> > > > > md.tpr> > > > I had (as expected) an error massage states that IRS is 
> > > > > not an energy > > group however if I have added IRS as an energy 
> > > > > group I had an error that > > some atoms are in multiple energy Mon. 
> > > > > groups.> > > > Well, what is IRS? Is it a protein, another molecule? 
> > > > > You've got very > different groups labeled for energy monitoring and 
> > > > > energygrp-excl, so something > needs to be fixed. Without any clue 
> > > > > what exactly you're dealing with, it's hard > to give any useful 
> > > > > information.> 
 
 
IRS is a group of residues in the protein, suppose that my protein has 50 
residues, IRS is a group that contains residues 2, 7, 9, 15, 45 for example. So 
the IRS group is actually part of my protein
Now I have four groups the SOL, ligand (T27), protein and IRS which overlapped 
with the protein (this is the problem) ...
I need to fix the position of IRS residues and exclude the non-bonding 
interactions between these residues and the solvent. Gromacs will not accept 
IRS as an energy group because there will be some residues that are common with 
the protein and so I can't state it in the energy exclusions??
 

 > > *So, my first question is how to deal with that problem for including my > 
 > > > frozen residues that way?*> > > > * *> > > > 2*.* The second method I 
 > > think about is to just position-restrained > > these residues where I have 
 > > created an .itp file for the residues need > > to be fixed (POSRE_IRS.itp) 
 > > using/ genpr /command. But I don’t know how > > to consider that in the 
 > > calculations….> > > > *Can I just include this file in the toplogy file 
 > > (#include > > “POSRE_IRS.itp”) and add the line Define = -DPOSRE_IRS in my 
 > > .mdp file??*> > > > Look in your protein topology (if you created one with 
 > > pdb2gmx) to get the > syntax right, because, as written no, your approach 
 > > will not work. If you > always #include "POSRE_IRS.itp," then position 
 > > restraints are always applied. > To make them conditional> > #ifdef 
 > > POSRE_IRS> #include "POSRE_IRS.itp"> #endif> 
 
 
That's fine... so if I just add unconditional #include "POSRE_IRS.itp" to the 
.top file Gromacs will apply postion restraints even without adding the define 
line to the .mdp file?
 
 
 
 
> -Justin> > > * *> > > > Looking forward for your kind suggestions and 
> comments> > > > > > > > Great Thanks> > > > Mohammed
 
**Mohammed K. Abdel-HamidPhD 
CandidateSchool of Chemistry University of Wollongong Northfields Ave. 
Wollongong, NSW, 2522
Ph:  +61 2 4221 3510Fax: +61 2 4221 4287 
_
Time for change? Find your ideal job with SEEK.
http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Fninemsn%2Eseek%2Ecom%2Eau%2F%3Ftracking%3Dsk%3Atl%3Ask%3Anine%3A0%3Ahottag%3Achange&_t=757263783&_r=SEEK_tagline&_m=EXT___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] MD vs Scattering

[Justin A. Lemkul]

Chih-Ying Lin wrote:
 
 
Hi

Can we simulate "samlple putting on the equipment using GROMACS-MD package"?
 


This question doesn't make any sense to me.  If you can explain the procedure 
you are interested in simulating, you might be able to get more useful advice.


-Justin

 
Thank you

Lin




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--


Justin A. Lemkul
Graduate Research Assistant
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] RE: Is there any option to output interaction energy based on energy groups?

[Vitaly Chaban]

>   Is there any option to output  total  interaction energy
> (without *internal
> energy*)  based on energy groups?

I don't know such. But it seems very easy to sum the terms which are
output.


===
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] RE: Constant Velocity

[Vitaly Chaban]

gurgo> Hello all,

gurgo> Is there anyway to provide constant velocity to any particular group of 
atoms.?

See acc-grps





===
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] MD vs Scattering

[Chih-Ying Lin]

Hi
Can we simulate "samlple putting on the equipment using GROMACS-MD package"?


Thank you
Lin
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Is there any option to output interaction energy based on energy groups?

[Liu Shiyong]

Hi,

  Is there any option to output  total  interaction energy
(without *internal
energy*)  based on energy groups?


*g_energy -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr*

[shiy...@reco temp20090115]$ g_energy -f
r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr
 :-)  G  R  O  M  A  C  S
(-:

 Gnomes, ROck Monsters And Chili Sauce

:-)  VERSION 4.0.2  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

   :-)  g_energy  (-:

Option Filename  Type Description

  -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr  Input
   Energy file: edr ene
 -f2   ener.edr  Input, Opt.  Energy file: edr ene
  -s  topol.tpr  Input, Opt.  Run input file: tpr tpb tpa
  -o energy.xvg  Output   xvgr/xmgr file
-viol  violaver.xvg  Output, Opt. xvgr/xmgr file
-pairspairs.xvg  Output, Opt. xvgr/xmgr file
-oraorienta.xvg  Output, Opt. xvgr/xmgr file
-ortorientt.xvg  Output, Opt. xvgr/xmgr file
-odaorideva.xvg  Output, Opt. xvgr/xmgr file
-odroridevr.xvg  Output, Opt. xvgr/xmgr file
-odtoridevt.xvg  Output, Opt. xvgr/xmgr file
-otenoriten.xvg  Output, Opt. xvgr/xmgr file
-corr   enecorr.xvg  Output, Opt. xvgr/xmgr file
-vis  visco.xvg  Output, Opt. xvgr/xmgr file
-ravg  runavgdf.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint19  Set the nicelevel
-b   time   0   First frame (ps) to read from trajectory
-e   time   0   Last frame (ps) to read from trajectory
-[no]w   bool   no  View output xvg, xpm, eps and pdb files
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]fee bool   no  Do a free energy estimate
-fetemp  real   300 Reference temperature for free energy
calculation
-zeroreal   0   Subtract a zero-point energy

-[no]sum bool   no  Sum the energy terms selected rather than
display
them all

-[no]dp  bool   no  Print energies in high precision

-[no]mutot   bool   no  Compute the total dipole moment from the

components

-[no]uni bool   yes Skip non-uniformly spaced frames

-skipint0   Skip number of frames between data points

-[no]averbool   no  Print also the X1,t and sigma1,t, only if only 1

energy is requested

-nmolint1   Number of molecules in your sample: the energies

are divided by this number

-ndf int3   Number of degrees of freedom per molecule.

Necessary for calculating the heat capacity

-[no]flucbool   no  Calculate autocorrelation of energy fluctuations

rather than energy itself

-[no]orinst  bool   no  Analyse instantaneous orientation data

-[no]ovecbool   no  Also plot the eigenvectors with -oten

-acflen  int-1  Length of the ACF, default is half the number of

frames

-[no]normalize bool yes Normalize ACF

-P   enum   0   Order of Legendre polynomial for ACF (0
indicates
none): 0, 1, 2 or 3

-fitfn   enum   noneFit function: none, exp, aexp, exp_exp, vac,

exp5, exp7 or exp9

-ncskip  int0   Skip N points in the output file of correlation

functions
-beginfitreal   0   Time where to begin the exponential fit of the
correlation function
-endfit  real   -1  Time where to end the exponential fit of the
correlation function, -1 is till the end

Opened r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr as single
precision energy file

Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
---
  1  G96Bond  2  G96Angle 3  Proper-

[gmx-users] Constant Velocity

[avinash kumar]

Hello all,

Is there anyway to provide constant velocity to any particular group of atoms.?

-- 
Avinash Kumar.
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

[Justin A. Lemkul]

Liu Shiyong wrote:
Thanks. 

I used the PDB file with H .  It works though it's still a mystery for 
me why PDB file without H couldn't work.
 


Because the atoms will be numbered wrong.  When you use pdb2gmx, hydrogens will 
be added to some groups (polar groups, aromatics, N-termini, etc).  So, starting 
with chain A, which now has three additional protons on the N, the numbering 
will be very different from the original pdb file.  Check out each .pdb file and 
your topologies and see for yourself how quickly the numbering differs.


-Justin




On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul > wrote:




Liu Shiyong wrote:



The problem lies here:


Including chain 1 in system: 1296 atoms 125 residues
Including chain 2 in system: 1274 atoms 123 residues
Including chain 3 in system: 2085 atoms 201 residues

This suggests that chain 2 (Protein B) should contain numbers up to
about 2500.


   ATOM   1996  O   ASN B 248  49.634   9.874  85.195
 1.00  0.00
   ATOM   1997  OXT ASN B 248  50.217  10.536  83.158
 1.00  0.00
   TER
   ATOM   1998  N   GLY C 249  70.273  30.186  73.098
 1.00  0.00
   ATOM   1999  CA  GLY C 249  68.973  30.327  72.421
 1.00  0.00


This is the original .pdb file, then?  The hydrogens will be missing
from the appropriate groups in the pdb2gmx-processed output
structures.  You can check the numbering (and pertinent charge
groups) in the topology for each chain, to be sure.


  make_ndx -f ${df}.pdb  -o ${file}.ndx >
   ${file}.output.make_ndx
  << _EOF_
  del 0-9
  chain A and B
  chain C
  q
  _EOF_


This should work, with the right input :)

-Justin


-- 



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin






--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu  (shiyong...@ku.edu 
 or liushiy...@ku.edu )

Homepage: http://www.people.ku.edu/~syliu
Lab:http://vakser.bioinformatics.ku.edu/people
Phone:  (785) 864-1962


--


Justin A. Lemkul
Graduate Research Assistant
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

[Liu Shiyong]

Thanks.

I used the PDB file with H .  It works though it's still a mystery for me
why PDB file without H couldn't work.



On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul  wrote:

>
>
> Liu Shiyong wrote:
>
> 
>
> The problem lies here:
>
> Including chain 1 in system: 1296 atoms 125 residues
> Including chain 2 in system: 1274 atoms 123 residues
> Including chain 3 in system: 2085 atoms 201 residues
>
> This suggests that chain 2 (Protein B) should contain numbers up to about
> 2500.
>
> ATOM   1996  O   ASN B 248  49.634   9.874  85.195  1.00  0.00
>>ATOM   1997  OXT ASN B 248  50.217  10.536  83.158  1.00  0.00
>>TER
>>ATOM   1998  N   GLY C 249  70.273  30.186  73.098  1.00  0.00
>>ATOM   1999  CA  GLY C 249  68.973  30.327  72.421  1.00  0.00
>>
>>
> This is the original .pdb file, then?  The hydrogens will be missing from
> the appropriate groups in the pdb2gmx-processed output structures.  You can
> check the numbering (and pertinent charge groups) in the topology for each
> chain, to be sure.
>
>make_ndx -f ${df}.pdb  -o ${file}.ndx >
>>${file}.output.make_ndx
>>   << _EOF_
>>   del 0-9
>>   chain A and B
>>   chain C
>>   q
>>   _EOF_
>>
>
> This should work, with the right input :)
>
> -Justin
>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>



-- 
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu (shiyong...@ku.edu or liushiy...@ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:http://vakser.bioinformatics.ku.edu/people
Phone:  (785) 864-1962
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

[Justin A. Lemkul]

Liu Shiyong wrote:



The problem lies here:

Including chain 1 in system: 1296 atoms 125 residues
Including chain 2 in system: 1274 atoms 123 residues
Including chain 3 in system: 2085 atoms 201 residues

This suggests that chain 2 (Protein B) should contain numbers up to about 2500.


ATOM   1996  O   ASN B 248  49.634   9.874  85.195  1.00  0.00
ATOM   1997  OXT ASN B 248  50.217  10.536  83.158  1.00  0.00
TER
ATOM   1998  N   GLY C 249  70.273  30.186  73.098  1.00  0.00
ATOM   1999  CA  GLY C 249  68.973  30.327  72.421  1.00  0.00



This is the original .pdb file, then?  The hydrogens will be missing from the 
appropriate groups in the pdb2gmx-processed output structures.  You can check 
the numbering (and pertinent charge groups) in the topology for each chain, to 
be sure.



   make_ndx -f ${df}.pdb  -o ${file}.ndx >
${file}.output.make_ndx
   << _EOF_
   del 0-9
   chain A and B
   chain C
   q
   _EOF_


This should work, with the right input :)

-Justin

--


Justin A. Lemkul
Graduate Research Assistant
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Software Raid and low GROMACS performance

[Martin Höfling]

Am Dienstag, den 20.01.2009, 17:07 -0200 schrieb Alexandre Suman de
Araujo:

> I have two machines with Intel Quad Core processors and Intel 
> motherboards. In the first one I'm running Open Suse with normal 
> partition scheme. In the second I'm running Ubuntu 8.04 with software 
> RAID 1.

Hard disk IO should not limit scaling and simulations at all (in most
cases...).

> Running a simulations in parallel (4 process, one for each core) in the 
> first computer I have a scaling of almost 100%. The same simulation in 
> the second computer gives me a very worst scaling.

In principle, software RAID and RAID functions implemented in
chipsets/BIOS require the CPU. Although RAID 1 should be pretty
inexpensive and even RAID 5 should create high load in most MD
scenarios.

> Is it possible that the software RAID is the responsible for this lost 
> in GROMACS performance? Does anybody have experience with this?

Is the rest of the Hardware comparable? To further test impact of your
RAID, you can easily disable RAID 1 by (temporarily) remove one of the
disks.

Best
Martin


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Software Raid and low GROMACS performance

[Alexandre Suman de Araujo]

Hi all.

I have two machines with Intel Quad Core processors and Intel 
motherboards. In the first one I'm running Open Suse with normal 
partition scheme. In the second I'm running Ubuntu 8.04 with software 
RAID 1.


Running a simulations in parallel (4 process, one for each core) in the 
first computer I have a scaling of almost 100%. The same simulation in 
the second computer gives me a very worst scaling.


Is it possible that the software RAID is the responsible for this lost 
in GROMACS performance? Does anybody have experience with this?


Thank's

--
**
Alexandre Suman de Araujo*
Faculdade de Ciências Farmacêuticas de Ribeirão Preto*
Universidade de São Paulo*
Dep. de Física e Química *
Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.su...@gmail.com  *
CEP: 14040-903* Phone: +55 (16) 3602-4172*
Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222*
** 


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] RE: Numbering in xtc and in conf.gro. Does it coincide?

[Vitaly Chaban]

>>
>> In other words, is information about the initial (in conf.gro)
>> numbering of molecules present in the xtc trajectory file? Looking at
>> the xtc using gmxdump I see the numbering always start with zero in
>> spite of the xtc-qrps arguments.
>> 
> All files number from 0 to natom-1. You have to do the remapping.

And the sequence of the groups in the xtc file is defined by the order
in xtc-grps. Right?


===
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

[Justin A. Lemkul]

Liu Shiyong wrote:

Hi
I have checked the manual, but it did not help. Checking the cgnr column 
did not help either.


Well, did it indicate that these atoms are indeed in the same charge group?  I 
suggested before that you check out your topology to see how grompp is 
interpreting it.  If, as you say, these chains should be separate, then why is 
grompp thinking they are in a joined molecule?  What command did you give pdb2gmx?


What I do is just splitting the pdb file into two energy groups (chains 
A+B and C). I do not change any definitions of charge groups in Gromacs.

As the result, I am getting "1996 and 1998 are in different energy groups".

ATOM   1996  O   ASN B 248  49.634   9.874  85.195  1.00  0.00
ATOM   1997  OXT ASN B 248  50.217  10.536  83.158  1.00  0.00
TER
ATOM   1998  N   GLY C 249  70.273  30.186  73.098  1.00  0.00
ATOM   1999  CA  GLY C 249  68.973  30.327  72.421  1.00  0.00

As you see, atoms 1996 and 1998 should be in different groups. I have no 
any idea whether
it's related to Gromacs or to the pdb file, or to something else? Could 
anybody advice SOMETHING?




Again, check the topology to see what pdb2gmx gave you.  Consider what you did 
at the pdb2gmx step.  Does it help to process each chain separately and, for 
example:


#include "Protein_A.itp"
#include "Protein_B.itp"
#include "Protein_C.itp"

...in the topol.top?

-Justin




On Mon, Jan 19, 2009 at 11:59 AM, Justin A. Lemkul > wrote:




Liu Shiyong wrote:


Hi,

 I searched the mail list.
 I found a solution to define energy groups by chain.

make_ndx -f ${df}.pdb  -o ${file}.ndx > ${file}.output.make_ndx
<< _EOF_
del 0-9
chain A and B
chain C
q
_EOF_

But , I run
grompp -maxwarn 10 -f em.mdp -c ${file}.gro -n ${file}.ndx -p
${file}.top -po ${file}.mdout.mdp -o${file}.input.tpr

and got  error information:

---
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150

Fatal error:
atoms 1996 and 1998 in charge group 296 of molecule type
'Protein_B' are in different energy groups
---

I checked my *.ndx file:

1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993
1994 1995
1996 1997
[ chC ]
1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
2011 2012
2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025
2026 2027


 1996 and 1998 are in different energy groups.

What is  the meaning of  " the charge group 296 of molecule type
'Protein_B'  "?


The manual has information about charge groups.  To see exactly what
you've split apart, check your topology (cgnr column).

-Justin



On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   Liu Shiyong wrote:

   Hi,

We have a protein with two chains A and B. We want to
calculate
   the interaction energy only.
   Would you advise how to define the energy groups for the
chains
   and how to output the interaction
   energy between chains A and B ?


   Have a search of the mailing list archives, similar questions
have
   been dealt with there. Also look in the manual for energy
groups in
   several places.

   Mark
   ___
   gmx-users mailing listgmx-users@gromacs.org

   >

   http://www.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search before
   posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to gmx-users-requ...@gromacs.org

   >.

   Can't post? Read http://www.gromacs.org/mailing_lists/users.php




-- 
Shiyong Liu

Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: sy...@ku.edu  > (shiyong...@ku.edu
 > or liushiy...@ku.edu
 >)

Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

[Liu Shiyong]

Hi
I have checked the manual, but it did not help. Checking the cgnr column did
not help either.
What I do is just splitting the pdb file into two energy groups (chains A+B
and C). I do not change any definitions of charge groups in Gromacs.
As the result, I am getting "1996 and 1998 are in different energy groups".

ATOM   1996  O   ASN B 248  49.634   9.874  85.195  1.00  0.00
ATOM   1997  OXT ASN B 248  50.217  10.536  83.158  1.00  0.00
TER
ATOM   1998  N   GLY C 249  70.273  30.186  73.098  1.00  0.00
ATOM   1999  CA  GLY C 249  68.973  30.327  72.421  1.00  0.00

As you see, atoms 1996 and 1998 should be in different groups. I have no any
idea whether
it's related to Gromacs or to the pdb file, or to something else? Could
anybody advice SOMETHING?



On Mon, Jan 19, 2009 at 11:59 AM, Justin A. Lemkul  wrote:

>
>
> Liu Shiyong wrote:
>
>>
>> Hi,
>>
>>  I searched the mail list.
>>  I found a solution to define energy groups by chain.
>>
>> make_ndx -f ${df}.pdb  -o ${file}.ndx > ${file}.output.make_ndx << _EOF_
>> del 0-9
>> chain A and B
>> chain C
>> q
>> _EOF_
>>
>> But , I run
>> grompp -maxwarn 10 -f em.mdp -c ${file}.gro -n ${file}.ndx -p ${file}.top
>> -po ${file}.mdout.mdp -o${file}.input.tpr
>>
>> and got  error information:
>>
>> ---
>> Program grompp, VERSION 4.0.2
>> Source code file: grompp.c, line: 150
>>
>> Fatal error:
>> atoms 1996 and 1998 in charge group 296 of molecule type 'Protein_B' are
>> in different energy groups
>> ---
>>
>> I checked my *.ndx file:
>>
>> 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995
>> 1996 1997
>> [ chC ]
>> 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
>> 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027
>>
>>
>>  1996 and 1998 are in different energy groups.
>>
>> What is  the meaning of  " the charge group 296 of molecule type
>> 'Protein_B'  "?
>>
>>
> The manual has information about charge groups.  To see exactly what you've
> split apart, check your topology (cgnr column).
>
> -Justin
>
>
>>
>> On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham 
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>Liu Shiyong wrote:
>>
>>Hi,
>>
>> We have a protein with two chains A and B. We want to calculate
>>the interaction energy only.
>>Would you advise how to define the energy groups for the chains
>>and how to output the interaction
>>energy between chains A and B ?
>>
>>
>>Have a search of the mailing list archives, similar questions have
>>been dealt with there. Also look in the manual for energy groups in
>>several places.
>>
>>Mark
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> Shiyong Liu
>> Postdoc
>> center for bioinformatics in the university of kansas
>> Lab: (785)864-1962
>> Email: sy...@ku.edu  (shiyong...@ku.edu > shiyong...@ku.edu> or liushiy...@ku.edu )
>> Homepage: http://www.people.ku.edu/~syliu
>> Lab:http://vakser.bioinformatics.ku.edu/people
>> Phone:  (785) 864-1962
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Sh

Re: [gmx-users] Numbering in xtc and in conf.gro. Does it coincide?

[David van der Spoel]

Vitaly Chaban wrote:

Source code file: matio.c, line: 533

Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00


Although nclust.xvg, maxclust.xvg, avclust.xvg are created and seem
adequate.

However what could the above error indicate?



that all atoms belong to the same cluster.


Yes, it's true in my case.


And one more question about index file. If xtc-qrps is used and only
the groups of interest are output in xtc file, should the atoms in the
index file be renumbered or not?

For example, if in conf.gro we have atoms of interest with numbers 4,5,6
and didn't write atoms 1,2,3 to the xtc file, should we then refer to the
wanted atoms as 4,5,6 (as it was initially) or 1,2,3 (due to the
shift...)?

In other words, is information about the initial (in conf.gro)
numbering of molecules present in the xtc trajectory file? Looking at
the xtc using gmxdump I see the numbering always start with zero in
spite of the xtc-qrps arguments.


All files number from 0 to natom-1. You have to do the remapping.


Thank you.
Vitaly


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Numbering in xtc and in conf.gro. Does it coincide?

[Vitaly Chaban]

> Source code file: matio.c, line: 533
> 
> Fatal error:
> Lo: 0.00, Mid: 1.00, Hi: 1.00
> 
> 
> Although nclust.xvg, maxclust.xvg, avclust.xvg are created and seem
> adequate.
> 
> However what could the above error indicate?

>that all atoms belong to the same cluster.

Yes, it's true in my case.


And one more question about index file. If xtc-qrps is used and only
the groups of interest are output in xtc file, should the atoms in the
index file be renumbered or not?

For example, if in conf.gro we have atoms of interest with numbers 4,5,6
and didn't write atoms 1,2,3 to the xtc file, should we then refer to the
wanted atoms as 4,5,6 (as it was initially) or 1,2,3 (due to the
shift...)?

In other words, is information about the initial (in conf.gro)
numbering of molecules present in the xtc trajectory file? Looking at
the xtc using gmxdump I see the numbering always start with zero in
spite of the xtc-qrps arguments.


Thank you.
Vitaly


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] electric field effects

[rams rams]

Dear users,

Does any one aware of how to carry out the simulations in presence of a
static and oscillating electric fields ? I found an option E_x, E_y, E_z
needed to be mentioned in the run mdp file. Other than this are there any
thing we need to mention ?

Ram.
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] deform option in parallel with Gromacs 4.0.2

[Berk Hess]

Hi,

This bug has been fixed in 4.0.3,
but I forgot about it when writing the release notes.

Berk

> From: ydub...@uvm.edu
> To: gmx-users@gromacs.org
> Date: Tue, 20 Jan 2009 08:53:15 -0500
> Subject: [gmx-users] deform option in parallel with Gromacs 4.0.2
> 
> Hi,
> 
> I am running stress simulations of vesicles and lipid bilayer  
> membranes, which work on one processor but fail when using multiple  
> processors. The simulations run Marrink's CGMD model with Gromacs  
> 4.0.2 (sorry I am unable to upgrade until next week) on openmpi and  
> mpich. The simulations run fine with the deform option set to zero for  
> all six components but crashes for 2 processors or more. Here is an  
> example of what I get on a mac with openmpi (fink package of gromacs):
> [ip138195:37938] *** Process received signal ***
> [ip138195:37938] Signal: Segmentation fault (11)
> [ip138195:37938] Signal code: Address not mapped (1)
> [ip138195:37938] Failing at address: 0x8fe830
> [ip138195:37938] [ 0] 2   libSystem.B.dylib
> 0x925882bb _sigtramp + 43
> [ip138195:37938] [ 1] 3   ???  
> 0x 0x0 + 4294967295
> [ip138195:37938] [ 2] 4   libgmx_mpi.5.dylib   
> 0x003d24f1 do_nonbonded + 1361
> [ip138195:37938] *** End of error message ***
> [ip138195:37939] *** Process received signal ***
> [ip138195:37939] Signal: Segmentation fault (11)
> [ip138195:37939] Signal code: Address not mapped (1)
> [ip138195:37939] Failing at address: 0xfb890
> [ip138195:37939] [ 0] 2   libSystem.B.dylib
> 0x925882bb _sigtramp + 43
> [ip138195:37939] [ 1] 3   ???  
> 0x 0x0 + 4294967295
> [ip138195:37939] [ 2] 4   libgmx_mpi.5.dylib   
> 0x003d24f1 do_nonbonded + 1361
> [ip138195:37939] *** End of error message ***
> mpiexec noticed that job rank 0 with PID 37938 on node  
> ip138195.uvm.edu exited on signal 11 (Segmentation fault).
> 1 additional process aborted (not shown)
> I have checked the wiki, manuals and searched this list but I can't  
> find any report of bugs nor an indication that I am doing something  
> wrong. It seems that there might be a bug associated with the deform  
> option in parallel.
> Thanks for any insight, advice on this.
> 
> .
>   --
> Yves Dubief, Ph.D., Assistant Professor
> Graduate program coordinator
> University of Vermont, School of Engineering
> Mechanical Engineering Program
> 201 D Votey Bldg, 33 Colchester Ave, Burlington, VT 05405
> Tel: (1) 802 656 1930 Fax: (1) 802 656 3358
> Also:
> Vermont Advanced Computing Center
> 206 Farrell Hall, 210 Colchester Ave, Burlington, VT 05405
> Tel: (1) 802 656 9830 Fax: (1) 802 656 9892
> email: ydub...@uvm.edu
> web: http://www.uvm.edu/~ydubief/
> 
> 
> 
> 
> 
> 
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_
What can you do with the new Windows Live? Find out
http://www.microsoft.com/windows/windowslive/default.aspx___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] RE: How to output a single index group

[Omer Markovitch]

Also check out "make_ndx -help". Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Mon, Jan 19, 2009 at 18:28, Vitaly Chaban  wrote:

> > I am running a simulation of 5 time steps and am trying to avoid
> setting
> > nstxtcout = 1 or nstxout = 1.  The file size becomes unmanageable if I
> set
> > either of these two parameters to 1.  I do not need the coordinates for
> all
> > atoms in the system, just the alpha carbons, which are grouped in the
> index
> > file, but I do need coordinates for each time step.  Is there any way of
> > specifying in the parameter file to only output the coordinates for the
> alpha
> > carbons?  Thanks!
>
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] deform option in parallel with Gromacs 4.0.2

[Yves Dubief]

Hi,

I am running stress simulations of vesicles and lipid bilayer  
membranes, which work on one processor but fail when using multiple  
processors. The simulations run Marrink's CGMD model with Gromacs  
4.0.2 (sorry I am unable to upgrade until next week) on openmpi and  
mpich. The simulations run fine with the deform option set to zero for  
all six components but crashes for 2 processors or more. Here is an  
example of what I get on a mac with openmpi (fink package of gromacs):

[ip138195:37938] *** Process received signal ***
[ip138195:37938] Signal: Segmentation fault (11)
[ip138195:37938] Signal code: Address not mapped (1)
[ip138195:37938] Failing at address: 0x8fe830
[ip138195:37938] [ 0] 2   libSystem.B.dylib
0x925882bb _sigtramp + 43
[ip138195:37938] [ 1] 3   ???  
0x 0x0 + 4294967295
[ip138195:37938] [ 2] 4   libgmx_mpi.5.dylib   
0x003d24f1 do_nonbonded + 1361

[ip138195:37938] *** End of error message ***
[ip138195:37939] *** Process received signal ***
[ip138195:37939] Signal: Segmentation fault (11)
[ip138195:37939] Signal code: Address not mapped (1)
[ip138195:37939] Failing at address: 0xfb890
[ip138195:37939] [ 0] 2   libSystem.B.dylib
0x925882bb _sigtramp + 43
[ip138195:37939] [ 1] 3   ???  
0x 0x0 + 4294967295
[ip138195:37939] [ 2] 4   libgmx_mpi.5.dylib   
0x003d24f1 do_nonbonded + 1361

[ip138195:37939] *** End of error message ***
mpiexec noticed that job rank 0 with PID 37938 on node  
ip138195.uvm.edu exited on signal 11 (Segmentation fault).

1 additional process aborted (not shown)
I have checked the wiki, manuals and searched this list but I can't  
find any report of bugs nor an indication that I am doing something  
wrong. It seems that there might be a bug associated with the deform  
option in parallel.

Thanks for any insight, advice on this.

.
 --
Yves Dubief, Ph.D., Assistant Professor
Graduate program coordinator
University of Vermont, School of Engineering
Mechanical Engineering Program
201 D Votey Bldg, 33 Colchester Ave, Burlington, VT 05405
Tel: (1) 802 656 1930 Fax: (1) 802 656 3358
Also:
Vermont Advanced Computing Center
206 Farrell Hall, 210 Colchester Ave, Burlington, VT 05405
Tel: (1) 802 656 9830 Fax: (1) 802 656 9892
email: ydub...@uvm.edu
web: http://www.uvm.edu/~ydubief/







___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] RE: Tcl script

[Vitaly Chaban]

> I just now started with TCL scripting.And it will be helpful if  someone
> tell me how to write a TCL script for the following queries.?


> 2. what is the total charge of the protein?

Yeah, Tcl is a good way to write scripts for gromacs but it is really
not a part of the package. :)

As for the protein, just look at your topology. Probably you will not even
need a script...


===
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_clussize. strange error

[David van der Spoel]

Vitaly Chaban wrote:

Hi,

I have a system with three kinds of particles. For this time I want to examine
possible clusters containing only two kinds of particles. My index file 
consists of all
the numbers of those atoms which belong to the particles of interest.
Then
g_clustsize(402) -n index.ndx

It seems to work correctly but after reading the trajectory gives an
error:

Program g_clustsize_402f, VERSION 4.0.2
Source code file: matio.c, line: 533

Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00


Although nclust.xvg, maxclust.xvg, avclust.xvg are created and seem
adequate.

However what could the above error indicate?


that all atoms belong to the same cluster.



Thanks.


===
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] g_clussize. strange error

[Vitaly Chaban]

Hi,

I have a system with three kinds of particles. For this time I want to examine
possible clusters containing only two kinds of particles. My index file 
consists of all
the numbers of those atoms which belong to the particles of interest.
Then
g_clustsize(402) -n index.ndx

It seems to work correctly but after reading the trajectory gives an
error:

Program g_clustsize_402f, VERSION 4.0.2
Source code file: matio.c, line: 533

Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00


Although nclust.xvg, maxclust.xvg, avclust.xvg are created and seem
adequate.

However what could the above error indicate?

Thanks.


===
Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] About frozen groups

[Justin A. Lemkul]

Mohammed Kamal wrote:


Tcoupl   = berendsen

tau_t= 0.1 0.1 0.1 0.1

tc_grps  = protein T27 SOL Cl ; T27 is the ligand


General advice: do not couple solvent and ions separately.  I believe there is a 
newer version of the tutorial that fixes this information.  See here:


http://wiki.gromacs.org/index.php/thermostats



ref_t= 300 300 300 300

*energygrps   = protein T27 SOL *

*energygrp_excl   = IRS IRS IRS SOL*

*freezegrps   = IRS*

*freezedim= Y Y Y*

Pcoupl   = berendsen

pcoupltype   = isotropic

tau_p= 0.5

compressibility  = 4.5e-5

ref_p= 1.0

gen_vel  = yes

gen_temp = 300

gen_seed = 173529

 


and when I used the grommp line of

*grompp* -f md.mdp -c 2zd1_eq.gro -p 2zd1.top -n IRS.ndx -o md.tpr

I had (as expected) an error massage states that IRS is not an energy 
group however if I have added IRS as an energy group I had an error that 
some atoms are in multiple energy Mon. groups.




Well, what is IRS?  Is it a protein, another molecule?  You've got very 
different groups labeled for energy monitoring and energygrp-excl, so something 
needs to be fixed.  Without any clue what exactly you're dealing with, it's hard 
to give any useful information.


*So, my first question is how to deal with that problem for including my 
frozen residues that way?*


* *

2*.* The second method I think about is to just position-restrained 
these residues where I have created an .itp file for the residues need 
to be fixed (POSRE_IRS.itp) using/ genpr /command. But I don’t know how 
to consider that in the calculations….


*Can I just include this file in the toplogy file (#include 
“POSRE_IRS.itp”) and add the line Define = -DPOSRE_IRS in my .mdp file??*




Look in your protein topology (if you created one with pdb2gmx) to get the 
syntax right, because, as written no, your approach will not work.  If you 
always #include "POSRE_IRS.itp," then position restraints are always applied. 
To make them conditional


#ifdef POSRE_IRS
#include "POSRE_IRS.itp"
#endif

-Justin


* *

Looking forward for your kind suggestions and comments

 


Great Thanks

Mohammed



Download free emoticons today! Holiday cheer from Messenger. 



Find great deals on eBay Net yourself a bargain 






___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--


Justin A. Lemkul
Graduate Research Assistant
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

RE: [gmx-users] Tcl script

[Kukol, Andreas]

Tcl is not part of Gromacs. Please direct your enquiry to the appropriate 
mailing list, e.g.

http://www.tcl.tk/community/

Andreas


From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of varsha gautham
Sent: 20 January 2009 07:05
To: gmx-users@gromacs.org
Subject: [gmx-users] Tcl script

I just now started with TCL scripting.And it will be helpful if  someone tell 
me how to write a TCL script for the following queries.?

Given a ubiquitin protein ,

1.what is the end-to-end distance ( c-terminal and N-termnal) distance of ubq 
and how does it change with time?
2. what is the total charge of the protein?
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php