Re: [gmx-users] problem with dimer simulation !

try - cluster, and then as cluster group protein.Kay.On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote: hi, all user:   i performed the dimer simulation,  and want to realize the interaction between two peptides. but frequently, i  encountered this kind of problem:  sometimes peptides moved out of the

Re: [gmx-users] center of mass pulling in AFM

, Berk Hess wrote: From: Kay Gottschalk <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] center of mass pulling in AFM Date: Tue, 18 Jul 2006 14:41:53 +0200 Ok, that's what we thought. So would you think

Re: [gmx-users] center of mass pulling in AFM

Would you agree with that? Thanks, Kay. On Jul 18, 2006, at 2:16 PM, Berk Hess wrote: From: Kay Gottschalk <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] center of mass pulling in AFM Date: Tue, 18 Jul 200

Re: [gmx-users] center of mass pulling in AFM

, but artificially ) elongated due to the COM fixing. Did I understand that correctly? Thanks, Kay. On Jul 18, 2006, at 11:31 AM, Berk Hess wrote: From: Kay Gottschalk <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: [gmx-

[gmx-users] center of mass pulling in AFM

Hi there, we are doing pulling simulations of protein complexes. For these simulations, we keep the COM of one group fixed and pull on the COM of the other group. Now we got into this discussion, whether this introduces artificial distortions on the hold protein. If the protein deforms in

Re: [gmx-users] g_dist

t each step. Just a thought. --- Xavier Periole <[EMAIL PROTECTED]> wrote: Kay Gottschalk wrote: They are not interacting. The distance is larger than 40 Å. But still,if the distance to the mirror image is 41 Å and to the same protein in the box is 45 Å, the distance to the mirror im

Re: [gmx-users] g_dist

yep, thanks! K. On May 22, 2006, at 6:15 PM, Xavier Periole wrote: Kay Gottschalk wrote: They are not interacting. The distance is larger than 40 Å. But still,if the distance to the mirror image is 41 Å and to the same protein in the box is 45 Å, the distance to the mirror image will

Re: [gmx-users] g_dist

Periole wrote: Kay Gottschalk wrote: Hi there, we are doing a pulling simulation and want to monitor the distance between two atoms during pulling. Using g_dist the distance is calculated between all mirror images of the periodic boundary conditions, and the minimal distance is calculated

Re: [gmx-users] To add all hydrogens

Depends on the force field. Take opls/aa for all hydrogens.Best,Kay.On May 22, 2006, at 3:52 PM, <[EMAIL PROTECTED]> wrote:Dear All, First of all, I would like to give my thanks for the help David van der Spoel has given us. I'm doing an energy minimization with mdrun without problems. However, I

[gmx-users] g_dist

Hi there, we are doing a pulling simulation and want to monitor the distance between two atoms during pulling. Using g_dist the distance is calculated between all mirror images of the periodic boundary conditions, and the minimal distance is calculated. In our case, this is uncomfortable,

Re: [gmx-users] g_rdf on Mac OS X 10.3, 10.4

(1/nm)"}, {"-energy", FALSE, etREAL, {&energy}, "Energy of the incoming X-ray (keV) "} }; #define NPA asize(pa) char *fnTPS,*fnNDX; bool bSQ,bRDF; t_filenm fnm[] = { { efTRX, "-f", NULL, ffREAD }, { efTPS, NULL, NULL,