Re: [gmx-users] Warning with L-BFGS minimization

Mark Abraham wrote: > Jochen Hub wrote: >> Hi, >> >> with l-bfgs minimzation, grompp always reports >> >> WARNING 1 [file em.mdp, line unknown]: >> For efficient BFGS minimization, use switch/shift/pme instead of >> cut-off. >> >> e

[gmx-users] Warning with L-BFGS minimization

= 1. I could't find anything on that in the archive. Is that a known issue? Cheers, Jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goett

Re: [gmx-users] spliting clusters.pdb

sts 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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dyna

Re: [gmx-users] range of gen_seed

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.ph

Re: [gmx-users] trjconv in Parallel run

e 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] How to confine a protein in a box?

rs > 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] I am not able to write the cyclohexane topology files

st. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group A

[gmx-users] posres problem in 4.0_rc2. Bug in grompp?

-mdrun, the error occurs. Or do I miss something? cheers, Jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel

Re: [gmx-users] Performance problems with more than one node

to do it. Hi, you can count the nr of atoms in the structure: grep -c ATOM protein.pdb Jochen > > Thanks, I will look at some of his posts. > > Best regards, > > Tiago Marques > > > On Tue, Sep 23, 2008 at 4:03 PM, Jochen Hub <[EMA

Re: [gmx-users] Performance problems with more than one node

ests 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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dy

Re: [gmx-users] tpbconv*

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? Re

Re: [gmx-users] Calculating Temperature from Velocity

interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biom

Re: [gmx-users] output format of gromacs utilities

print $2}' > yy$nr fi done out=${1%%.xvg}.dat paste -d ' ' times.tmp yy[0-9][0-9][0-9][0-9][0-9] > $out echo created ${1%%.xvg}.dat > > I experience difficulties to read such (xvg) format by sigmaplot. > > -- Dr.

Re: [gmx-users] Cann't get the same result ?

sers@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

Re: [gmx-users] TIP4P and TIP5P

hive 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] ask for help

gt; 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] Leaflet of Bilayer

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 -- Dr. Jochen Hub Max Planck Institu

Re: [gmx-users] harmonic restraint

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/mailin

Re: [gmx-users] topology of cyclohexane

HB1 CB HB2 CB CC CC HC1 CC HC2 CC CD CD HD1 CD HD2 CD CE CE HE1 CE HE2 CE CF CF HF1 CF HF2 Vitaly Chaban wrote: > Guys, > > Does anybody have an already prepared topology of cyclohexane? > > Thanks. > -- *****

Re: [gmx-users] POPC number

ace or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecula

Re: [gmx-users] POPC number

tp://www.gromacs.org/mailing_lists/users.php > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (

Re: [gmx-users] POPC number

the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11

Re: [gmx-users] to add counter ions based on potential

end it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynam

Re: [gmx-users] removing degrees of freedome from different proteins at different timesteps of an md simulation

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 > > . > -- Dr. Jochen Hub Max Planck Institute for Biophysical Che

Re: [gmx-users] printing coords ; energies

://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 -- Dr. Joch

[gmx-users] genbox and triclinic boxes. Problem an workaround.

oblem occurs in the 3.3.1 and in a quite recent CVS version (3.3.99_development_20080718). Best, Jochen -- ******** Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Ge

Re: [gmx-users] How to use g_energy after parellal mdrun

extend the PR. Best, Jochen With Thanks, Vivek 2008/8/27 Jochen Hub <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> vivek sharma wrote: Hi There, I am running gromacs in a parellel architecture using -np 20. Now I want to generate the energy plot using g

Re: [gmx-users] Warnings while grompp_d

o the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- **** Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fas

Re: [gmx-users] How to use g_energy after parellal mdrun

/users.php -- **** Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)55

Re: [gmx-users] when gen_vel should be "no"

/users.php -- **** Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)55

Re: [gmx-users] Visualizing gromacs result

efore 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 -- ******** Dr. Jochen Hub Max Planck Institute for Biophy

Re: [gmx-users] Re: Simulations backward in time

he initial velocities. Shouldn't that be the same as using a negative dt ? jochen -- ******** Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gw

[gmx-users] Fitting when structure and reference are slightly different

to start a simulation from the fitted structure. Thanks a lot, Jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel

Re: [gmx-users] PDBs for mixed lipid bilayer/membrane

g! 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 . -- ************ Dr. Jochen Hub Max Planck Institute for Bioph

Re: [gmx-users] Position Constraint

nd it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- ******** Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Ge

Re: [gmx-users] regarding rmsd !!

s.org/mailing_lists/users.php -- ******** Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.:

Re: [gmx-users] forward and reverse free energy not consistant

cribe 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 -- ************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dyna

Re: [gmx-users] still problems with dodecahedron box and editconf

s 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 -- ******** Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics gro

Re: [gmx-users] membrane stabilisation

dimensions as a function of time with g_energy. cheers, jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551

Re: [gmx-users] problem regarding protein in water simulation

://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 -- ******** Jochen Hub Max Planck Ins

Re: [gmx-users] "Lam" is not required for running parallel job

gromacs.org/mailing_lists/users.php . -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettin

Re: [gmx-users] comm_grps

Read http://www.gromacs.org/mailing_lists/users.php . -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[

Re: [gmx-users] Cuted trr file not readable

extended xtc, trr and edr just change t_init in the mdp file. Cheers, Jochen -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germa

Re: [gmx-users] interchain bond

list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- **** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassber

Re: [gmx-users] about details of the topology file.

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] Problems with GROMPP

e the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-3

Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

_lists/users.php -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___

Re: [gmx-users] Umbrella Sampling options

he reference group", so, that's just what you want, isn't it? Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dyna

Re: [gmx-users] output coordinate file of ionic system

re 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] HELP REGARDING COMMAND g_pvd

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 . -- ******** Jochen Hub Max Planck Institute for Biophysical

Re: [gmx-users] problem with WHAM

us to help you. And maybe the command line and the head of your pdo file. Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gw

Re: [gmx-users] insert protein in membrane

ciate your help! /Magnus -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de __

Re: [gmx-users] AEDANS & DDPM

nd it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ************ Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen,

Re: [gmx-users] g_potential problem

PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de

Re: [gmx-users] membrane protein

/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 -- ************ Jochen Hub Max Planck

Re: [gmx-users] How to choose lipid molecules?

e found in "Bioelectrochemistry of Membranes", edited by Walz, Teissie, Milazzo. And there are dozens of reviews on membrane channels. Check google scholar. Cheers, Jochen > > Really thanks for your help, and i hope i would not be bothering you. > > Best regards, >

Re: [gmx-users] How to choose lipid molecules?

t; Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am F

Re: [gmx-users] Re: Density Deferences between spc216 and tip4p

hu, 13 Dec 2007 10:28:02 +0100 From: Jochen Hub <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p water models To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=fl

Re: [gmx-users] Density Deferences between spc216 and tip4p water models

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 . -- ******** Jochen Hub Max Planck Institute for Biophysical

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

27;t rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computation

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

r giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11

[gmx-users] Gel Phase in DMPC using Berger force field ??

t lot, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gw

Re: [gmx-users] Rerefence on Berendsen vs Nose-Hoover

97 Department of Chemistry, Stanford University | Lab fax : 650.724.4021 http://www.dillgroup.ucsf.edu/~jchodera Date: Mon, 15 Oct 2007 15:37:40 +0200 From: Jochen Hub <[EMAIL PROTECTED]> Subject: To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; ch

[gmx-users] Rerefence on Berendsen vs. Nose-Hoover

Hi, I think there is a paper around which says that for parcticle purposes it hardly matters whether one uses Berendsen or Nose-Hoover T-coupling. Does anyone remember the reference? Thanks in advance, Jochen -- Jochen Hub Max Planck

[gmx-users] Rerefence on Berendsen vs Nose-Hoover

Hi, I think there is a paper around which says that for parcticle purposes it hardly matters whether one uses Berendsen or Nose-Hoover T-coupling. Does anyone remember the reference? Thanks in advance, Jochen -- Jochen Hub Max Planck

[gmx-users] OPLS parametes for cholesterol

Hi, does anyone know if there are is an OPLS topology for cholesterol around. Thanks a lot in advance, Jochen & Plamen -- **** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-3

[gmx-users] parameters of hydrogen peroxide H2O2

properly. Thanks a lot in advance, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de

[gmx-users] parameters for nitric oxide (NO)

Dear gromacs users, does anyone know if there are parameters for nitric oxide (NO) published somewhere? Thanks in advance, jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am

Re: [gmx-users] OPLS-AA Charge Calculation

EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Em

Re: [gmx-users] Box vector question

ling_lists/users.php -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de _

Re: [gmx-users] editconf

_lists/users.php -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de _

Re: [gmx-users] trjconv problem

3.3.1. cheers, jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gw

Re: [gmx-users] Stepsize too small, or no change in energy

n)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 -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular d

Re: [gmx-users] oplsaa and lincs error

EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[

Re: [gmx-users] N/A

/listinfo/gmx-users 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 -- ******** Jochen Hub Max Planck Institute for B

Re: [gmx-users] Re: Can not open file: topol.tpr

e: I ran mpirun mdrun from inside the folder where topol.tpr was, so unless i have to specify the path explicitly i think it should have to see that file. any other ideas? Thank you very much ! -- Guillem Plasencia From: Jochen Hub <[EMAIL PROTECTED]> Reply-To: Discussion list fo

Re: [gmx-users] Can not open file: topol.tpr

ww.gromacs.org/mailman/listinfo/gmx-users 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 -- Jochen Hub Ma

Re: [gmx-users] comm-mode = Angular

ead http://www.gromacs.org/mailing_lists/users.php -- ************ Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germ

Re: [gmx-users] Imaging in PBC simulations

rotein and comm_mode = Linear or use trjconv with the -fit option and fit your protein on the starting position after finishing the simulation. Cheers, Jochen -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecul

Re: [gmx-users] Imaging in PBC simulations

rotein and comm_mode = Linear or use trjconv with the -fit option and fit your protein on the starting position after finishing the simulation. Cheers, Jochen -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecul

Re: [gmx-users] dumping energies

energy groups (some water molecules in your case) and this way get reasonable statistics. cheers, jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany

Re: [gmx-users] topology database

gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] How to install MPI version of GROMACS on a LINUX CLUSTER

www.gromacs.org/mailing_lists/users.php -- ******** Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email:

Re: [gmx-users] Re: LINCS Warning using mdrun

not stable (but I can't find out the reason) a comment would be highly appreciated Grazia Hi Grazia, I was wondering if your system converged to a low potential energy and low maximum force during energy minimization... Jochen -- J

Re: [gmx-users] Re: LINCS Warning using mdrun

anks Gaurav --- mdrun log file output -- Better show us the output of your energy minimization. The ouput of your md only shows that your sctructure has some serious problem...like your box is too small or whatever... Jochen -- ******** Jo

Re: [gmx-users] Parameters for OPLS

1.0 rvdw = 1.0 Temperature Coupling ist turne on (berendsen) and Pressure Coupling is turend off. The size of the box is 4x5.8x10 nm. thanks Kobi These are pretty much standart parameters, so they should be fine... -- ******** Jochen Hub Max Planc

Re: [gmx-users] LINCS Warning using mdrun

Fmax= 1.60758e+04, atom= 13032 Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de

Re: [gmx-users] Why my protein always falls out of the water box?

. good luck, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de

Re: [gmx-users] can not write a gro file without atom names

mailman/listinfo/gmx-users 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 -- ******** Jochen Hub Max Planck Instit

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