[gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

Hi everyone, I'm having problems running an md simulation (with gmx-4.0.2) using vsites and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem seems to occur when the molecule crosses pbc, since the first sign of the simulation not working fine after ~3ns is " Warning: 1-4 int

[gmx-users] (no subject)

Justin A. Lemkul wrote: > > > [EMAIL PROTECTED] wrote: >> >> Hi everyone, >> >> I'm having problems running an md simulation (with gmx-4.0.2) using vsites >> and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem >> seems to occur when the molecule crosses pbc, since the first

Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

--- Missatge original Assumpte: De: [EMAIL PROTECTED] Data: Tue, Novembre 25, 2008 9:52 am A:"Discussion list for GROMACS users" [EMAIL PROTECTED] --

Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

Hi everyone, As I wrote yesterday, I'm having problems running stable simulations with vsites and constraints in all bonds in different time-steps using gmx-4.0.2. As long as the dna strand does not cross pbc, the simulations run fine (the longest I did was 5ns). The dna topology was generated wit

[gmx-users] restarting REMD checkpoint gmx-cvs

Hi users, I would like to restart some REMD simulations done with the cvs code with the new checkpoint feature, but I'm unsure if I'm doing it right. Each replica has its own state#.cpt file, but it seems to me that the -cpi option of the cvs mdrun (at version 3.3.99_development_20080718) only a

Re: [gmx-users] converting parmbsc0 dihedrals to RB function

Hi, Right, the only dihedral angles that do not allow an exact translation to RB because of the phase are the ones involving the new parametrization for nucleic acids. Namely, it corrects the alpha/gamma transitions to get the populations of states right, thus avoiding the loss of helicity on th

[gmx-users] Re: converting parmbsc0 dihedrals to RB function

Hi Alan, I have no experience with acpypi, so I can't tell which one does better, or why... rdparm not being needed, that would be a strong point. Unfortunately, I'm running a bit short of time at the moment, so I can't really spend a lot of time looking into unknown codes, hope you understand...

Re: [gmx-users] protein in hole

Hi, Use editconf. You can center the protein and align its main axis ( -princ ) or play around with the rotation of the initial orientation ( -rotate ). Then get the surface of the correct (aligned and centered) oritentation as input for making the hole (if you want to use the modified md code).

Re: [gmx-users] g_wham and PMF problem

In the old version of gmx, and I think nobody changed a single line of code, this is the message you would get regardless of the file you input. Buggy, yes. Check the mailing list, check the code yourself, as you love to say. Guillem > >> Opening file pull1.pdo.gz. >> --