Re: [gmx-users] To deshuffle or not to deshuffle, that is a question.

Selon Yang Ye <[EMAIL PROTECTED]>: > Deshuffling shall be made before 2), 3) and 4). Furthermore, be aware that if you use the 'sort' option, you'll also need to desort ... IIRC, there is a g_desort program that does all in one (it was published on the list some time ago), and should be avaialbe

Re: [gmx-users] How to use PRODRG to help new user do gromacs?

Selon Yafei Dai <[EMAIL PROTECTED]>: > Hi, all, > I am a new user of gromacs and I read the manual and tutorial but I still get > confused. > I need your help. > > >From PRODRG, I got four *.top files, one *.itp file and three *.PDB files > and some other files. In my system, I don't have any solv

Re: [gmx-users] Implicit solvent simulation

Selon Erik Lindahl <[EMAIL PROTECTED]>: > Hi, > > On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote: > > > The version used by Alan Mark has never made it into gromacs. > > Rather, Erik Lindahl started the implementation of this stuff but > > did never finish it completely, due to other prior

Re: [gmx-users] Regarding mdrun segmentation fault in cluster

Selon naga raju <[EMAIL PROTECTED]>: > Dear gmx users, > I am using mdrun command in pentium-4 > redhat linux, job was completed without any errors. > When I use the same files in cluster(redhat > enterprizes OS), I got the following error, ... > gen_seed =17532 > cons

Re: [gmx-users] Stuck ...

Selon Tsjerk Wassenaar <[EMAIL PROTECTED]>: > Hi Stephane, > > I think this ends up in treating symptoms. Setting up a simulation of > HIVP should not give such problems. It's probably best to start all > over: pdb2gmx, EM in vacuum, editconf -d 1.0, genbox, EM in solvent, > etc... Keep track of e