Re: [gmx-users] Dimer simulation problem

.gromacs.org/mailman/listinfo/gmx-users> >>> Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>> posting! >>> Please don't post (un)subscribe reque

Re: [gmx-users] ED - Projecting on an eigenvector

I suppose you are writing a extr.pdb form g_anaeig. Try writing down extr. xtc and load it onto a pdb/gro using vmd. Then it should not be a problem. Best Wishes, Sarath > Did you make the molecules whole and removed jumps (in case of a multimer) > prior to filtering? > > Cheers, > > Tsjerk > >

Re: [gmx-users] hi

On 29 May 2011 14:45, wrote: > Hi all.. > I want to ask if it is possible to restart the md run if due to power > problem final md run not completed means initiating md from where is stop > due to any reason? > You can supply the checkpoint file written out, by -cpi option to mdrun and continue

RE: [gmx-users] Add custom residue to DNA index group

> > Thanks for the quick reply, > > I have already done that, and GROMACS, in all other cases, knows it is > DNA, as it automatically forms the bonds with other residues. > > it is only when it makes its index files that it doesnt know that my > residue is DNA. > Did you make the change in residue

Re: [gmx-users] simulation of membrane protein

On Wed, Dec 22, 2010 at 11:23 AM, shikha agarwal wrote: > I am trying to simulate a theorical model of a membrane protein in explicit > lipid bilayer membrane environment (DMPC or POPC), I have the pdb > files of this protein and membrane , I have to topolies files this > lipids (dmpc.

Re: [gmx-users] "freezegrps" concept

On Wed, Dec 15, 2010 at 12:53 AM, YUVRAJ UBOVEJA wrote: > Hello > > I am trying to simulate lipase in water in ffamber99sb-ildn. Chosen "cubic" > as box with distance of 1nm b/w solute n box. > Protein is going out of the box after equilibration step. Any solution? > > The protein does not diffuse