Re: [gmx-users] Segmentation fault with gromacs 3.3.3

It seems to be a problem related to the debian package. I have compiled gromacs 3.3.3 from source with gcc-4.3 and apparently the problem has dissapeared. Perhaps, the binaries on the debian package were compiled with gcc-4.1. Cesar Avila escribió: > Dear all, > I am new to the gromacs simulation

[gmx-users] Segmentation fault with gromacs 3.3.3

Dear all, I am new to the gromacs simulation package. Thus far I have been using Charmm and NAMD, but now I am interested on testing Marrink's Coarse-Grained Martini FF. I managed to setup an initial configuration for a protein in a water box. After a few minimization steps, I ran the simulation fo

[gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??

I was wondering why the Hydrogens from the non N-terminus NH2 group in the uncharged Lysine molecule had charges of 0.36 as specified by gromacs(H1 and H2) when the Jorgensen published value for H's in RCH2NH2 was 0.35.  All of the other charges in this molecule I have found in publications exce

Re[2]: [gmx-users] RE: can gmx be used to simulation NaCl

Tsjerk, Well, the best way would be AIMD, no doubt. William, Look here http://www.mpibpc.mpg.de/groups/grubmueller/start/teaching/vorlesung_computerbiophysik_2004/p4/index.html for an example how freezing/melting of argon is processed by means of GROMACS. TW> Hi William, TW> I'm not very sure y

Re: [gmx-users] High number of steps are adding

Hi Sudheer, I would say you just try to add a nanosecond to a run which still has ten to go (10+1=11). That also tells me you're not trying to extend a run already performed (properly), as it has a starting step of 0 (starting time 0.000). Then on another note, it seems that you didn't copy-paste

Re: [gmx-users] Magic number error

Hi Minnale, You could try another version as was suggested... Never hurts to try. The magic number error occurs if the file is screwed. trjconv will correctly process the trajectory up to the point where the magic number error occurs, so you can restart from the last good entry in the file. Out of

Re: [gmx-users] Protein is moving out of box.

Hi, Well, I think it should also be incorporated into (Gromacs) MD tutorial material. It's on my to do list. I don't think there's much use in adding a message in the mdrun output (might as well always add it, not even checking for jumps). It's basic PBC, which, with a bit of thinking, can be unde

Re: [gmx-users] RE: can gmx be used to simulation NaCl

Hi William, I'm not very sure you can simulate crystallization of salt with classical MD. In any case, the force field is not parameterized to reproduce crystallization or melting c.q. the melted state of NaCl. It's therefore unlikely that it will produce meaningful results. The best approach :) w

Re: [gmx-users] instalation in FC7i386

On Fri, 2008-06-27 at 18:24 -0400, Justin A. Lemkul wrote: > > Why do you want to use GCC 3.4 instead of the default compiler of the > > distribution which is GCC 4.1.2 invoked with gcc? > > > From the Downloads section of the home page: > > "WARNING: do not use the gcc 4.1.x set of compilers.