Re: [gmx-users] Re: Re: topology using prodrg (Diego Nolasco)

Take a look at John Kerrigan's tutorial? http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf And as said Justin, "There is no mention of Gromos87 in the topology line". Diego. 2008/7/6 h a <[EMAIL PROTECTED]>: > Yea I used the beta version and chose the force field GROMOS96.1. But after > I run

Re: [gmx-users] topology using prodrg

Are you sure you used prodrg beta? http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta 2008/7/4, h a <[EMAIL PROTECTED]>: > > Dear users, > > I am modeling polymer surface. I need topology for polystyrene. I used > prodrg earlier version and beta version but in both cases I get topology > for

Re: [gmx-users] topology for c-alpha protein model

After pdb2gmx of the whole structure, make an index file and them run another pdb2gmx choosing the c-alpha group. I hope it helps. 2008/6/20, Lillian Chong <[EMAIL PROTECTED]>: > > Dear Gromacs Users, > > I would like to generate a topology for a protein in which each > residue is represented only

Re: [gmx-users] REMD problems

k the log files, for there is written what > is not identical in one of your replicas. Look for > "XXX is not equal for all subsystems" > > Marcus > > > Diego Nolasco wrote: > > Dear gmx-users, > > > > I am facing some problems with replica e

[gmx-users] REMD problems

Dear gmx-users, I am facing some problems with replica exchange. Few seconds after the job submission it ends with the error below: " Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 8 --- Program m

Re: [gmx-users] how to run parallel jobs in gromacs

Did you booted your lam? Go to a specific node of your cluster, for example node 3, and create a file with a simple name like lamhosts. This file must contain just the nodes you may want to boot (the name of the node, like no3, or something like this). Than, run lamboot lamhosts -v If you have tw

Re: [gmx-users] how to run parallel jobs in gromacs

Hi there, Try giving the complete address of the command you want to run, just like this: /usr/bin/grompp -f *.mdp -c *.gro -p *.top -o *.tpr -np 4 mpirun -np 4 /usr/bin/mdrun_mpi.lam -s *.tpr -x *.xtc -c *.gro -g *.log -e *.edr -v The address depends on your installation. In my case is /usr/bi

Re: [gmx-users] FEP method in protein-ligand systems

r?hl=en&lr=&q=%22free+energy+perturbation%22&btnG=Search > ). > Lots of hits for alchemical free energy calculations and thermodynamic > integration as well. I'm not sure why you think there aren't many > publications on FEP. > > David > > > > Thanks

[gmx-users] FEP method in protein-ligand systems

in protein-ligand systems? Thanks a lot, Diego Nolasco ___ 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 pos