Re: [gmx-users] Why my system collapsed?

[Mark Abraham]

Peggy Yao wrote:

Dear all,
 
I've run this simulation twice, but got exactly the same error. 
Everything was fine up to position restrained simulation. However, the 
MD simulation was not successful. The final error is:
 
---

Program mdrun, VERSION 3.3.2
Source code file: nsgrid.c, line: 220
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Starting from step 1749465 (3498.93 ps), more and more bonds that 
rotated more than 30 degrees appeared. Starting from step 1749466, the 
warning "pressure scaling more than 1%, mu: 1.27191e+06 1.27191e+06 
1.27191e+06" started to appear, and the system collapsed at step 1749467.
 
Does anyone have idea what might be wrong? I was simulating a 
calcium-binding protein with calcium atoms in water for 4ns. Thanks!


http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25

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

Basically, there's something about your system setup (.mdp options, 
topology, starting structure) that leads to non-physical behaviour. Look 
closely at the early part of the simulation and see where things start 
going wrong. Pay attention to warnings from grompp - they're not decorative!


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 [EMAIL PROTECTED]

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

[gmx-users] Why my system collapsed?

[Peggy Yao]

Dear all,

I've run this simulation twice, but got exactly the same error. Everything
was fine up to position restrained simulation. However, the MD simulation
was not successful. The final error is:

---
Program mdrun, VERSION 3.3.2
Source code file: nsgrid.c, line: 220
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Starting from step 1749465 (3498.93 ps), more and more bonds that rotated
more than 30 degrees appeared. Starting from step 1749466, the warning
"pressure scaling more than 1%, mu: 1.27191e+06 1.27191e+06 1.27191e+06"
started to appear, and the system collapsed at step 1749467.

Does anyone have idea what might be wrong? I was simulating a
calcium-binding protein with calcium atoms in water for 4ns. Thanks!

Peggy
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Unable to compile Gromacs-CVS because calcpot.c

[Daniel Adriano Silva M]

Thanks David,
 as you addressed, adding  "NULL," at the end of the line 250 of
calcpot.c solved the compilation issue.

Daniel




2008/4/15 David van der Spoel <[EMAIL PROTECTED]>:
> Daniel Adriano Silva M wrote:
>
> > Hi there,
> >
> > I am tyring to compile CVS gromacs version "up-to-this-day",  and I
> > always finish with the same error (on two different machines), this
> > error is recurrent even if I use gcc or pathscale:
> >
>
>  edit the file, and on line 250 add at the end "NULL,"
>  and recompile. It may or may not crash genion.
>
> >
> >
> >
> >
> > # cc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/include/libxml2
> > -I../../include
> > -DGMXLIBDIR=\"/home/dsilva/PROGRAMAS/gromacs4_14-4-08/share/top\" -O3
> > -fomit-frame-pointer -finline-functions -Wall -Wno-unused
> > -malign-double -funroll-all-loops -MT calcpot.lo -MD -MP -MF
> > .deps/calcpot.Tpo -c calcpot.c -o calcpot.o
> > # calcpot.c: In function 'init_calcpot':
> > # calcpot.c:252: warning: passing argument 18 of 'init_md' from
> > incompatible pointer type
> > # calcpot.c:252: warning: passing argument 19 of 'init_md' from
> > incompatible pointer type
> > # calcpot.c:252: warning: passing argument 20 of 'init_md' from
> > incompatible pointer type
> > # calcpot.c:252: warning: passing argument 22 of 'init_md' from
> > incompatible pointer type
> > # calcpot.c:252: warning: passing argument 23 of 'init_md' from
> > incompatible pointer type
> > # calcpot.c:252: error: too few arguments to function 'init_md'
> > # make[3]: *** [calcpot.lo] Error 1
> > # make[3]: *** Se espera a que terminen otras tareas
> > # make[3]: se sale del directorio
> > `/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src/tools'
> > # make[2]: *** [all-recursive] Error 1
> > # make[2]: se sale del directorio
> > `/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src'
> > # make[1]: *** [all] Error 2
> > # make[1]: se sale del directorio
> > `/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src'
> > # make: *** [all-recursive] Error 1
> >
> >
> > any help will be welcome.
> >
> > Daniel S.
> > ___
> > 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 [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>  --
>  David van der Spoel, Ph.D.
>  Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>  Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>  [EMAIL PROTECTED][EMAIL PROTECTED]   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 [EMAIL PROTECTED]
>  Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] how to make choices of COM in the system with freeze group

[tuyusong]

Hi, Users,

I have a system with one carbon Nanotube and lots of water, in which
Nanotube is frozen. How do I remove the center-of-mass:

1) only remove the COM of SOL
2) remove both COM of SOL and CNT, separately
2) only remove the COM of "system" as a whole.

How do I make the choices?

Thank you very much!!!

Yusong.


-


___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Water flow through Carbon Nanotube

[Hero]

Hello, 

I am a new user of Gromacs and trying to simulate water 
flowing in nanotubes.

Can I get some idea on how to do this? Where can I have 
a sample?

Thank you very much!

Jue Chen


  

Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Minimize error

[Justin A. Lemkul]

> ---
> Program mdrun, VERSION 3.3.3
> Source code file: nsgrid.c, line: 226
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> Variable ci has value -2147483648. It should have been within [ 0 .. 3240 ]
>
> ---
>
> Does anyone know how can I fix it???

Yes, check the list archives and this link:

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

This error comes across the list almost weekly; you should be able to find a
solution in the archives.

-Justin

>
> Best Regard!
>
> Ana Carolina
>
>  between -00-00 and -99-99
> -
> Abra sua conta no Yahoo! Mail, o único sem limite de espaço para
> armazenamento!





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Unable to compile Gromacs-CVS because calcpot.c

[David van der Spoel]

Daniel Adriano Silva M wrote:

Hi there,

I am tyring to compile CVS gromacs version "up-to-this-day",  and I
always finish with the same error (on two different machines), this
error is recurrent even if I use gcc or pathscale:


edit the file, and on line 250 add at the end "NULL,"
and recompile. It may or may not crash genion.


# cc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/include/libxml2
-I../../include
-DGMXLIBDIR=\"/home/dsilva/PROGRAMAS/gromacs4_14-4-08/share/top\" -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-malign-double -funroll-all-loops -MT calcpot.lo -MD -MP -MF
.deps/calcpot.Tpo -c calcpot.c -o calcpot.o
# calcpot.c: In function 'init_calcpot':
# calcpot.c:252: warning: passing argument 18 of 'init_md' from
incompatible pointer type
# calcpot.c:252: warning: passing argument 19 of 'init_md' from
incompatible pointer type
# calcpot.c:252: warning: passing argument 20 of 'init_md' from
incompatible pointer type
# calcpot.c:252: warning: passing argument 22 of 'init_md' from
incompatible pointer type
# calcpot.c:252: warning: passing argument 23 of 'init_md' from
incompatible pointer type
# calcpot.c:252: error: too few arguments to function 'init_md'
# make[3]: *** [calcpot.lo] Error 1
# make[3]: *** Se espera a que terminen otras tareas
# make[3]: se sale del directorio
`/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src/tools'
# make[2]: *** [all-recursive] Error 1
# make[2]: se sale del directorio
`/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src'
# make[1]: *** [all] Error 2
# make[1]: se sale del directorio
`/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src'
# make: *** [all-recursive] Error 1


any help will be welcome.

Daniel S.
___
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 [EMAIL PROTECTED]

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



--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   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 [EMAIL PROTECTED]

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

[gmx-users] Minimize error

[Ana Carolina Sodero]

Hi!

I'm trying to minimize a protein into the box filled with solvent. 
I converted the pdb file into gro file, constructed a triclinic box (volume of 
~337 nm3) and filled with 9696 water molecules. I performed the minimization 
with 15 steps, using steepest descent integrator (mdp file enclosed).

title =  Yo
cpp =  /lib/cpp
define  =  -DFLEX_SPC
constraints   =  none
integrator =  steep
emtol   =  0.0001
emstep =  0.1
nstcgsteep=  100
nsteps  =  15
nstcomm  =  1
nstxout =  100
nstvout =  100
nstfout  =  0
nstlog   =  100
nstenergy  =  100
nstlist   =  10
ns_type =  grid
coulombtype  =  PME
rlist   =  0.9
rcoulomb   =  0.9
rvdw =  0.9
pme_order =  4
; Berendsen temperature coupling is on in four groups
Tcoupl  =  no
; Isotropic pressure coupling is now on
Pcoupl  =  no


For this particular simulation, the minimization process genarates an error 
message:

Getting Loaded...
Reading file sj2_steep.tpr, VERSION 3.3.3 (single precision)
Loaded with Money

Steepest Descents:
   Tolerance (Fmax)   =  1.0e-04
   Number of steps=   15
Step=0, Dmax= 1.0e-01 nm, Epot= -2.43719e+05 Fmax= 1.22008e+06, atom= 4686
Wrote pdb files with previous and current coordinates
Step=1, Dmax= 1.0e-01 nm, Epot= -2.74902e+05 Fmax= 1.82701e+05, atom= 14670

Back Off! I just backed up step1.pdb to ./#step1.pdb.1#
Wrote pdb files with previous and current coordinates
Step=2, Dmax= 1.2e-01 nm, Epot= -3.14226e+05 Fmax= 1.01056e+05, atom= 14672

Back Off! I just backed up step2.pdb to ./#step2.pdb.1#
Wrote pdb files with previous and current coordinates
Step=3, Dmax= 1.4e-01 nm, Epot= -3.45258e+05 Fmax= 8.00739e+04, atom= 18315

Back Off! I just backed up step3.pdb to ./#step3.pdb.1#
Wrote pdb files with previous and current coordinates
Step=4, Dmax= 1.7e-01 nm, Epot= -3.66329e+05 Fmax= 5.66550e+04, atom= 10626

Back Off! I just backed up step4.pdb to ./#step4.pdb.1#
Wrote pdb files with previous and current coordinates
Step=5, Dmax= 2.1e-01 nm, Epot= -1.37090e+23 Fmax= inf, atom= 5356

---
Program mdrun, VERSION 3.3.3
Source code file: nsgrid.c, line: 226

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 3240 ]

---

Does anyone know how can I fix it???

Best Regard!

Ana Carolina

 between -00-00 and -99-99   
-
Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! ___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Unable to compile Gromacs-CVS because calcpot.c

[Daniel Adriano Silva M]

Hi there,

I am tyring to compile CVS gromacs version "up-to-this-day",  and I
always finish with the same error (on two different machines), this
error is recurrent even if I use gcc or pathscale:

# cc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/include/libxml2
-I../../include
-DGMXLIBDIR=\"/home/dsilva/PROGRAMAS/gromacs4_14-4-08/share/top\" -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-malign-double -funroll-all-loops -MT calcpot.lo -MD -MP -MF
.deps/calcpot.Tpo -c calcpot.c -o calcpot.o
# calcpot.c: In function 'init_calcpot':
# calcpot.c:252: warning: passing argument 18 of 'init_md' from
incompatible pointer type
# calcpot.c:252: warning: passing argument 19 of 'init_md' from
incompatible pointer type
# calcpot.c:252: warning: passing argument 20 of 'init_md' from
incompatible pointer type
# calcpot.c:252: warning: passing argument 22 of 'init_md' from
incompatible pointer type
# calcpot.c:252: warning: passing argument 23 of 'init_md' from
incompatible pointer type
# calcpot.c:252: error: too few arguments to function 'init_md'
# make[3]: *** [calcpot.lo] Error 1
# make[3]: *** Se espera a que terminen otras tareas
# make[3]: se sale del directorio
`/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src/tools'
# make[2]: *** [all-recursive] Error 1
# make[2]: se sale del directorio
`/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src'
# make[1]: *** [all] Error 2
# make[1]: se sale del directorio
`/home/dsilva/PROGRAMAS/gromacs4_14-4-08/gmx/src'
# make: *** [all-recursive] Error 1


any help will be welcome.

Daniel S.
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] crash with LINCS WARNING

[Hannes Loeffler]

On Mon, 2008-04-14 at 19:22 -0400, LeeHwan-kyu wrote:
> Dear GMX-uers,
> 
> I'm simulating alpha-hemolysin channel in DMPC bilayer and water
> (using MARTINI protein FF), and my system keeps crashing with error
> below (even with very low timestep).

I suspect your problem is the MARTINI protein force field.  You need to
tell us more how you set up the .itp file.  Do you use dihedral terms
for extended sheets?  Replacing them with elastic bonds may help to
avoid problems with LINCS.  BTW, what is the very low timestep you
mentioned above?

Hannes.

___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] make_ndx for separating all atoms in two monolayers in a bilayer

[Ananya Debnath]

Hi,

I want to create an index file which will contain indices of all the
atoms in two monolayers separately in a bilayer. For this purpose
I have copied a python script from a post in gromacs mailing list, and
did a simple modification. But after modification, make_ndx gives
me error like "Group 1 does not exist" though output from the .py looks alright.

If someone gives me the idea why this occurs, it will be a great help.
The script I am running is as follows:
--

#!/usr/bin/python

import sys,string

# Usage with a pipe:
# python dppc_index.py dppc_npat.pdb |  make_ndx -f dppc_npat.pdb -o
dppc_bilayer.ndx
#


# main #

# print usage
if len(sys.argv) < 2:
sys.exit("Usage: dppc_index.py dppc_npat.pdb")

# define reference atom
REF_ATOM = "P8"

# read data
file = open(sys.argv[1],"r")
lines = file.readlines()
file.close()

# get Z mean (see
http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_62.html for
pdb file format)
Zsum = 0.0
nP = 0
for i in lines:
if i[:6] == "ATOM  " and string.split(i[12:16])[0] == REF_ATOM:
Zsum += float(i[46:54])
nP += 1
Zmean = Zsum / float(nP)

# get upper and lower leaflet
lower = []
upper = []
for i in lines:
if i[:6] == "ATOM  " and string.split(i[12:16])[0] == REF_ATOM:
atom_num = int(i[6:11])
Z = float(i[46:54])
if Z < Zmean:
   for j in range(-7,43):
  lower.append(atom_num+j)

if Z > Zmean:for j in range(-7,43):
  upper.append(atom_num+j)

 # print output for make_ndx
output = "keep 0\ndel 0\n"
output += "a "
for i in range(len(lower)):
if i < len(lower)-1:
output += "%i | a" % lower[i]
else:
output += "%i" % lower[i]
output += "\nname 0 lower_leaflet\n"
output += "a "
for i in range(len(upper)):
if i < len(upper)-1:
output += "%i | a" % upper[i]
else:
output += "%i" % upper[i]
output += "\nname 1 upper_leaflet\n"
output += "q\n"
print output,

--

 Thanks and Regards,
 Ananya.
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] calculating CD spectra

[Mark Abraham]

Marieke Schor wrote:

Hi,

I would like to calculate CD spectra from my simulation input and results
(41 amino acid protein simulated in GROMOS or OPLS force field).
Apparently this can be done with the MATMAC program (Fleischhauer et al.
1991; Daura et al. 2003). Are there better options (which?) and if not,
could someone help me to find this MATMAC program?


How about a (Google) search for papers that use it, or contacting the 
authors on the email address in the paper?


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 [EMAIL PROTECTED]

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

Re: [gmx-users] xpm2ps help

[Justin A. Lemkul]

Quoting "Rigden, LucianeVMello" <[EMAIL PROTECTED]>:

> Dear all,
>
> I am working with gromacs 3.3.3
>
> Trying to analyse possible changes in the secondary structure of the peptide
> along the simulation.
>
> do_dssp -f traj.xtc -s topol.tpr -sc -dt 5
> 1 protein

I believe the proper analysis should be done on Group 5, 'MainChain.'  Probably
xpm2ps cannot process the dssp output if you've analyzed the whole Protein.

-Justin

>
> xpm2ps -f ss.xpm
>
> There are 1 matrices in ss.xpm
> Matrix 0 is 20001 x 12
> zsh: segmentation fault  xpm2ps -f ss.xpm
>
>
> Any help?
> if xpm2ps is really a problem, as I had already noticed other people
> complains in the past, is there an alternative way to analyse it?
>
> Thanks in advance for your help.
> Luciane
>
> Dr Luciane Vieira de Mello
> School of Biological Sciences
> Room 2.20, Life Science Building
> Tel:(+44) 151 795 5140
> FAX:(+44) 151 794 5130
> University of Liverpool
> Crown St.,Liverpool L69 7ZB, U.K.
>
>
>
> -Original Message-
> From: [EMAIL PROTECTED] on behalf of
> [EMAIL PROTECTED]
> Sent: Thu 3/13/2008 12:12 AM
> To: gmx-users@gromacs.org
> Subject: gmx-users Digest, Vol 47, Issue 39
>
> Send gmx-users mailing list submissions to
>   gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>   http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>   [EMAIL PROTECTED]
>
> You can reach the person managing the list at
>   [EMAIL PROTECTED]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: trjconv output at a specified time (Liu Shiyong)
>2. Re: problem with mpi configuration. (Diego Enry)
>3. Re: trjconv output at a specified time (Alan Dodd)
>
>
> --
>
> Message: 1
> Date: Wed, 12 Mar 2008 18:24:00 -0500
> From: "Liu Shiyong" <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] trjconv output at a specified time
> To: "Discussion list for GROMACS users" 
> Message-ID:
>   <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset="utf-8"
>
> Thanks.
>
> The trajectory starts at 125ps ?
>
> So  step 1  == 125 ps
>   step 2 ==   250 ps
>   step 3  ==  375 ps
>
> Where is 125ps from ?
>
> But
>
> ; RUN CONTROL PARAMETERS
> integrator   = steep
> ; Start time and timestep in ps
> tinit= 0
> dt   = 0.002
>
>
>
> On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:
>
> > You asked for the frame at 1ps.  The trajectory starts at 125ps, so
> > unsurprisingly the program does not give you an output.
> >
> > - Original Message 
> > From: Liu Shiyong <[EMAIL PROTECTED]>
> > To: Discussion list for GROMACS users 
> > Sent: Wednesday, March 12, 2008 10:07:17 PM
> > Subject: [gmx-users] trjconv output at a specified time
> >
> > Hi,
> >
> > I want to output a structure in a given time, for example , in step 1
> > during minimization.
> >
> > I tried the following command using dump:
> > trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb  -s
> > r-l_1_oplsaa.input.tpr  -t0 0 -dump 1
> >
> > But It didnot work.
> >
> > Output msg:
> >
> > Select a group: 2
> > Selected 2: 'Protein-H'
> > trn version: GMX_trn_file (single precision)
> > Reading frame   0 time  125.000
> > Back Off! I just backed up m.pdb to ./#m.pdb.1#
> > Last frame 19 time 2418.000
> >
> > WARNING no output, trajectory ended at 2418
> >
> >
> > gcq#76: "Baseball Heroes Only" (P.J. Harvey)
> >
> > Best
> >
> > --
> > Shiyong Liu
> > Research Assistant
> > center for bioinformatics in the university of kansas
> > Lab: (785)864-1962
> > Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
> > Homepage:
> http://www.people.ku.edu/~syliu
> > Lab: http://vakser.bioinformatics.ku.edu/people
> > Phone: (785) 864-1962
> >
> >
> > -Inline Attachment Follows-
> >
> > ___
> > 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 [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> > __
> > Do You Yahoo!?
> > Tired of spam? Yahoo! Mail has the best spam protection around
> > http://mail.yahoo.com
> >
> > ___
> > 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

Re: [gmx-users] density and CG MARTINI force field

[Mark Abraham]

merc mertens wrote:

Dear people,

I am trying to use the MARTINI CG force field from Marrink et al. for a 100 
residue protein in water. I use the tools from the Marrink website 
(http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the 
necessary gro and itp files. For solvation of my protein I use the water.gro 
from the same website. However, using editconf/genbox to do so it is difficult 
to judge the density of system. genbox tells me that it is usually around a 
value between 220 and 260 g/l depending on boxsize. As the MARTINI forcefield 
uses a 1-to-4 mapping I think 250 g/l should correspond to 1000 g/l using an 
all-atom representation of my system. Still, I do not know whether these 
density values given by genbox are correct. Is there anyway to check this?


Your structure file should have the size of the box recorded - life is 
easy if it is cubic. Otherwise, add up your molecules and molar masses 
and invoke Avogadro for the mass.


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 [EMAIL PROTECTED]

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

Re: [gmx-users] log file has converted into.log.swp file

[Mark Abraham]

Anamika Awasthi wrote:

Dear Gromacs Users,

 Please help me to recover my important log file from swap file, How can 
I do this?

I am wondering wheather I can get my original file or not.



Swap file ".md2.log.swp" already exists!
[O]pen Read-Only, (E)dit anyway, (R)ecover, (Q)uit:


This is what (R)ecover does. You can protect yourself by copying these 
files somewhere else first. However you won't be able to get access to 
anything other than the contents of .md2.log.swp or .md2.log since 
nothing else exists.


Make backups!

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 [EMAIL PROTECTED]

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

Re: [gmx-users] xpm2ps help

[David van der Spoel]

Rigden, LucianeVMello wrote:



Dear all,

I am working with gromacs 3.3.3

Trying to analyse possible changes in the secondary structure of the 
peptide along the simulation.


do_dssp -f traj.xtc -s topol.tpr -sc -dt 5
1 protein

xpm2ps -f ss.xpm 


There are 1 matrices in ss.xpm
Matrix 0 is 20001 x 12
zsh: segmentation fault  xpm2ps -f ss.xpm



OS, compiler?

If it is reproducible on different computer systems you can upload a 
bugzilla. You can view the xpm file with the Gimp.



Any help?
if xpm2ps is really a problem, as I had already noticed other people 
complains in the past, is there an alternative way to analyse it?


Thanks in advance for your help.
Luciane

Dr Luciane Vieira de Mello   
School of Biological Sciences
Room 2.20, Life Science Building

Tel:(+44) 151 795 5140
FAX:(+44) 151 794 5130
University of Liverpool
Crown St.,Liverpool L69 7ZB, U.K.



-Original Message-
From: [EMAIL PROTECTED] on behalf of 
[EMAIL PROTECTED]

Sent: Thu 3/13/2008 12:12 AM
To: gmx-users@gromacs.org
Subject: gmx-users Digest, Vol 47, Issue 39

Send gmx-users mailing list submissions to
gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit
http://www.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
[EMAIL PROTECTED]

You can reach the person managing the list at
[EMAIL PROTECTED]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


Today's Topics:

   1. Re: trjconv output at a specified time (Liu Shiyong)
   2. Re: problem with mpi configuration. (Diego Enry)
   3. Re: trjconv output at a specified time (Alan Dodd)


--

Message: 1
Date: Wed, 12 Mar 2008 18:24:00 -0500
From: "Liu Shiyong" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] trjconv output at a specified time
To: "Discussion list for GROMACS users" 
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="utf-8"

Thanks.

The trajectory starts at 125ps ?

So  step 1  == 125 ps
  step 2 ==   250 ps
  step 3  ==  375 ps

Where is 125ps from ?

But

; RUN CONTROL PARAMETERS
integrator   = steep
; Start time and timestep in ps
tinit= 0
dt   = 0.002



On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:

 > You asked for the frame at 1ps.  The trajectory starts at 125ps, so
 > unsurprisingly the program does not give you an output.
 >
 > - Original Message 
 > From: Liu Shiyong <[EMAIL PROTECTED]>
 > To: Discussion list for GROMACS users 
 > Sent: Wednesday, March 12, 2008 10:07:17 PM
 > Subject: [gmx-users] trjconv output at a specified time
 >
 > Hi,
 >
 > I want to output a structure in a given time, for example , in step 1
 > during minimization.
 >
 > I tried the following command using dump:
 > trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb  -s
 > r-l_1_oplsaa.input.tpr  -t0 0 -dump 1
 >
 > But It didnot work.
 >
 > Output msg:
 >
 > Select a group: 2
 > Selected 2: 'Protein-H'
 > trn version: GMX_trn_file (single precision)
 > Reading frame   0 time  125.000
 > Back Off! I just backed up m.pdb to ./#m.pdb.1#
 > Last frame 19 time 2418.000
 >
 > WARNING no output, trajectory ended at 2418
 >
 >
 > gcq#76: "Baseball Heroes Only" (P.J. Harvey)
 >
 > Best
 >
 > --
 > Shiyong Liu
 > Research Assistant
 > center for bioinformatics in the university of kansas
 > Lab: (785)864-1962
 > Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
 > Homepage: 
http://www.people.ku.edu/~syliu

 > Lab: http://vakser.bioinformatics.ku.edu/people
 > Phone: (785) 864-1962
 >
 >
 > -Inline Attachment Follows-
 >
 > ___
 > 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 [EMAIL PROTECTED]
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >
 >
 > __
 > Do You Yahoo!?
 > Tired of spam? Yahoo! Mail has the best spam protection around
 > http://mail.yahoo.com
 >
 > ___
 > 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 [EMAIL PROTECTED]
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >



--
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PRO

[gmx-users] density and CG MARTINI force field

[merc mertens]

Dear people,

I am trying to use the MARTINI CG force field from Marrink et al. for a 100 
residue protein in water. I use the tools from the Marrink website 
(http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the 
necessary gro and itp files. For solvation of my protein I use the water.gro 
from the same website. However, using editconf/genbox to do so it is difficult 
to judge the density of system. genbox tells me that it is usually around a 
value between 220 and 260 g/l depending on boxsize. As the MARTINI forcefield 
uses a 1-to-4 mapping I think 250 g/l should correspond to 1000 g/l using an 
all-atom representation of my system. Still, I do not know whether these 
density values given by genbox are correct. Is there anyway to check this?

Thanks for your help,
Merc
-- 
Pt! Schon vom neuen GMX MultiMessenger gehört?
Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] xpm2ps help

[Rigden, LucianeVMello]

Dear all,

I am working with gromacs 3.3.3

Trying to analyse possible changes in the secondary structure of the peptide 
along the simulation.

do_dssp -f traj.xtc -s topol.tpr -sc -dt 5
1 protein 

xpm2ps -f ss.xpm  

There are 1 matrices in ss.xpm
Matrix 0 is 20001 x 12
zsh: segmentation fault  xpm2ps -f ss.xpm


Any help?
if xpm2ps is really a problem, as I had already noticed other people complains 
in the past, is there an alternative way to analyse it?

Thanks in advance for your help.
Luciane

Dr Luciane Vieira de Mello
School of Biological Sciences 
Room 2.20, Life Science Building
Tel:(+44) 151 795 5140
FAX:(+44) 151 794 5130
University of Liverpool
Crown St.,Liverpool L69 7ZB, U.K.



-Original Message-
From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED]
Sent: Thu 3/13/2008 12:12 AM
To: gmx-users@gromacs.org
Subject: gmx-users Digest, Vol 47, Issue 39
 
Send gmx-users mailing list submissions to
gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit
http://www.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject or body 'help' to
[EMAIL PROTECTED]

You can reach the person managing the list at
[EMAIL PROTECTED]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


Today's Topics:

   1. Re: trjconv output at a specified time (Liu Shiyong)
   2. Re: problem with mpi configuration. (Diego Enry)
   3. Re: trjconv output at a specified time (Alan Dodd)


--

Message: 1
Date: Wed, 12 Mar 2008 18:24:00 -0500
From: "Liu Shiyong" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] trjconv output at a specified time
To: "Discussion list for GROMACS users" 
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="utf-8"

Thanks.

The trajectory starts at 125ps ?

So  step 1  == 125 ps
  step 2 ==   250 ps
  step 3  ==  375 ps

Where is 125ps from ?

But

; RUN CONTROL PARAMETERS
integrator   = steep
; Start time and timestep in ps
tinit= 0
dt   = 0.002



On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:

> You asked for the frame at 1ps.  The trajectory starts at 125ps, so
> unsurprisingly the program does not give you an output.
>
> - Original Message 
> From: Liu Shiyong <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users 
> Sent: Wednesday, March 12, 2008 10:07:17 PM
> Subject: [gmx-users] trjconv output at a specified time
>
> Hi,
>
> I want to output a structure in a given time, for example , in step 1
> during minimization.
>
> I tried the following command using dump:
> trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb  -s
> r-l_1_oplsaa.input.tpr  -t0 0 -dump 1
>
> But It didnot work.
>
> Output msg:
>
> Select a group: 2
> Selected 2: 'Protein-H'
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time  125.000
> Back Off! I just backed up m.pdb to ./#m.pdb.1#
> Last frame 19 time 2418.000
>
> WARNING no output, trajectory ended at 2418
>
>
> gcq#76: "Baseball Heroes Only" (P.J. Harvey)
>
> Best
>
> --
> Shiyong Liu
> Research Assistant
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
>
>
> -Inline Attachment Follows-
>
> ___
> 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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> __
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
>
> ___
> 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 [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Shiyong Liu
Research Assistant
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: [EMAIL PROTECTED] ([EMAIL PROTECTED] or [EMAIL PROTECTED])
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
-- next part --
An HTML attachment was scrubbed...
URL: 
http://w

[gmx-users] log file has converted into.log.swp file

[Anamika Awasthi]

Dear Gromacs Users,

 Please help me to recover my important log file from swap file, How can I
do this?
I am wondering wheather I can get my original file or not.
E325: ATTENTION
Found a swap file by the name ".md2.log.swp"
  owned by: anamika   dated: Wed Apr 16 04:21:09 2008
 file name: ~anamika/MD/cm_A/test/md2.log
  modified: no
 user name: anamika   host name: cdfd-grid-node16
process ID: 29468 (still running)
While opening file "md2.log"
 dated: Thu Mar 20 16:09:42 2008

(1) Another program may be editing the same file.
If this is the case, be careful not to end up with two
different instances of the same file when making changes.
Quit, or continue with caution.

(2) An edit session for this file crashed.
If this is the case, use ":recover" or "vim -r md2.log"
to recover the changes (see ":help recovery").
If you did this already, delete the swap file ".md2.log.swp"
to avoid this message.

Swap file ".md2.log.swp" already exists!
[O]pen Read-Only, (E)dit anyway, (R)ecover, (Q)uit:


Thanks in advance
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] gromacs analysis performance on a dual core suse box.

[Stéphane Téletchéa]

Florian Haberl a écrit :

Hi,

On Tuesday, 15. April 2008 10:15, himanshu khandelia wrote:

Hello,

I am using a dual core Xeon with 4 GB RAM to do some gromacs analysis
and want to know what is the limiting factor in my machine's
performance.

When I run, say, a trjconv command on a 2.3 GB trajectory, the rest of
my machine pretty much freezes up. A trjconv will use only 1 cpu, but
is it using all the memory of the machine as well for IO? If it is not
using all the memory, then why does the machine freeze? Of course, the
answers might lie in my local installation, but I was wondering if you
folks have some insights? I am running Suse 10.x.

A top command typically indicates a 20-35 % cpu usage while running
the trjconv.


is your data on the local machine or it is mounted over nfs?

Do you have gbit nics?

Normally 100mbit cards or slow nfs server are the limiting factor.

Greetings,

Florian


I'd bet for your hard drive limiting the troughput, hard drives are
really slow in comparison with memory and cpu speed.
The fact that your machine seems frozen is another link to that.

In order to get a better response (i.e not complete freeze of the
machine), you could try another kernel scheduler (see the kernel option
elevator), but this will be a compromise between responsiveness and
throughput.

Cheers,
Stéphane

--
Stéphane Téletchéa, PhD.  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901

___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] gromacs analysis performance on a dual core suse box.

[Florian Haberl]

Hi,

On Tuesday, 15. April 2008 10:15, himanshu khandelia wrote:
> Hello,
>
> I am using a dual core Xeon with 4 GB RAM to do some gromacs analysis
> and want to know what is the limiting factor in my machine's
> performance.
>
> When I run, say, a trjconv command on a 2.3 GB trajectory, the rest of
> my machine pretty much freezes up. A trjconv will use only 1 cpu, but
> is it using all the memory of the machine as well for IO? If it is not
> using all the memory, then why does the machine freeze? Of course, the
> answers might lie in my local installation, but I was wondering if you
> folks have some insights? I am running Suse 10.x.
>
> A top command typically indicates a 20-35 % cpu usage while running
> the trjconv.

is your data on the local machine or it is mounted over nfs?

Do you have gbit nics?

Normally 100mbit cards or slow nfs server are the limiting factor.

Greetings,

Florian
-- 
---
 Florian Haberl
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
---
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] calculating CD spectra

[Marieke Schor]

Hi,

I would like to calculate CD spectra from my simulation input and results
(41 amino acid protein simulated in GROMOS or OPLS force field).
Apparently this can be done with the MATMAC program (Fleischhauer et al.
1991; Daura et al. 2003). Are there better options (which?) and if not,
could someone help me to find this MATMAC program?

Thanks,
Marieke Schor



___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] gromacs analysis performance on a dual core suse box.

[himanshu khandelia]

Hello,

I am using a dual core Xeon with 4 GB RAM to do some gromacs analysis
and want to know what is the limiting factor in my machine's
performance.

When I run, say, a trjconv command on a 2.3 GB trajectory, the rest of
my machine pretty much freezes up. A trjconv will use only 1 cpu, but
is it using all the memory of the machine as well for IO? If it is not
using all the memory, then why does the machine freeze? Of course, the
answers might lie in my local installation, but I was wondering if you
folks have some insights? I am running Suse 10.x.

A top command typically indicates a 20-35 % cpu usage while running
the trjconv.

Thank you,

-Himanshu
___
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php