Re: [gmx-users] mdrun_mpi error

On 10/12/2011 7:54 PM, aiswarya pawar wrote: i used the option still i get the error as= /bin/sh ../../libtool --tag=CC --mode=compile mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/staff/sec/secdpal/soft/gromacs/share/top\" -I/home/staff/sec/secdpal/soft/include

Re: [gmx-users] Problem with GDP parameters generation

documentation). Don't stress too much about the charges - those that are suitable in the bound and unbound form will normally be different, and current methods can't access the former. Mark -- next part -- An HTML attachment was scru

Re: Re: [gmx-users] Problem with GDP parameters generation

inquiries about it > (after checking the documentation). > > Don't stress too much about the charges - those that are suitable in the > bound and unbound form will normally be different, and current methods > can't access the former. > > Mark > -- next p

Re: [gmx-users] No such moleculetype Na

Hi Setare, You should find the ions.itp file in your computer, open and see the exact name of sodium in this file. Use this name when using the command "genion". Good luck! Cuong 2011/12/10 Setare Jiji > Hi, > > I am running Tutorial 1: Lysozyme in > Water

[gmx-users] Re: gmx-users Digest, Vol 92, Issue 56

> ;qmmm calculation > > QMMM = yes > > QMMM-grps= QMatoms > > QMMMscheme = normal > > QMmethod = MP2 > > QMbasis = 3-21g > > QMcharge = 0 > > Q

Re: [gmx-users] No such moleculetype Na

Hi Setare, That tutorial is made for later gromacs versions, as stated at the beginning. The naming of ions has changed since 4.0.*. Cheers, Tsjerk On Dec 10, 2011 1:00 PM, "Setare Jiji" wrote: Hi, I am running Tutorial 1: Lysozyme in Water

[gmx-users] No such moleculetype Na

Hi, I am running Tutorial 1: Lysozyme in Water. I used 4-0-7 version and the sequence is true but in minimization energy step,I have this fatal error:   No such moleculetype Na so,what do I do? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

Re: [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

On 12/10/11 3:23 AM, Matthew Zwier wrote: Hi Ruhollah, A while ago on the list there was a discussion of extreme memory use and possibly-incorrect results from g_msd under some conditions. The problem could be worked around by imaging the trajectory with trjconv first to remove jumps across the

[gmx-users] qm/mm(orca/gromacs)

Dear Gromacs developers: I'm trying to run a QM-MM single point energy calculation on a structure (a small molecule with 50 water molecules with no pbc, no cutoff). I use orca for QM part amd gromacs for MM part. But when I run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly and te

Re: [gmx-users] mdrun_mpi error

i used the option still i get the error as= /bin/sh ../../libtool --tag=CC --mode=compile mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/staff/sec/secdpal/soft/gromacs/share/top\" -I/home/staff/sec/secdpal/soft/include -O3 -qarch=ppc64 -qtune=pwr5 -c -o vmdio.lo vmdio