[gmx-users] Gromacs to amber atom type

In God We Trust Hello GMX users Does anyone know a way to convert atom type of G43a1 to atom type of Amber96(parm96) automatically. Thank you very much in advance Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran

Re: [gmx-users] segmentation fault with fitted gro files

Marta Murcia wrote: Dear all, I am running a series of AFM simulations starting from different conformations taken from a trajectory (gmx 3.3). Everything works fine, but if I try to orient all the snapshots with respect to a reference (based on the protein superimposition) I get segmentation

[gmx-users] Problem with trjorder in 3.3.1

Dear all, I tried to used the program trjorder (in the version 3.3.1) like this: trjorder -f xtc_4.xtc -s tpr_4.tpr -n index.ndx -o ordered.xtc -b 0 -e 10 -r 0.3 But the program always output nshell.xvg file,without ordered.xtc file. And I also tried this program in 3.2.1 using the same

RE: [gmx-users] Problem with trjorder in 3.3.1

From: Hu Zhongqiao [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] Problem with trjorder in 3.3.1 Date: Sat, 20 May 2006 20:21:41 +0800 Dear all, I tried to used the program trjorder (in the version 3.3.1)

Re: [gmx-users] how to use g_sham ?

Liang wrote: Liang wrote: Dear all users : g_sham is a new program in 3.3 and i cant find any discussion about how to use in mailing lists, and i didnt catch the point about the instructions in user manual. Is it possible to draw pics about PMF or free energy landscape using some

Re: [gmx-users] segmentation fault with fitted gro files

Marta Murcia wrote: Hi again, sorry about that, what I meant is that before even doing grompp I am taking snaphots that I oriented with respect a particular conformation (with trajconv or vmd) so I use gro files for the afm pulling that correspond to fitted structures instead of the raw files

Re: [gmx-users] segmentation fault with fitted gro files

David van der Spoel wrote: Marta Murcia wrote: Hi again, sorry about that, what I meant is that before even doing grompp I am taking snaphots that I oriented with respect a particular conformation (with trajconv or vmd) so I use gro files for the afm pulling that correspond to fitted

Re: [gmx-users] segmentation fault with fitted gro files

This is the md.log, note that the problem is with SOL (namely water) t = 0.000 ps: Water molecule starting at atom 171088 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Large VCM(group Protein): 0.0,

Re: [gmx-users] segmentation fault with fitted gro files

Marta Murcia wrote: This is the md.log, note that the problem is with SOL (namely water) t = 0.000 ps: Water molecule starting at atom 171088 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Large VCM(group Protein):

Re: [gmx-users] microcanonical

karamyog singh wrote: I guess since after the first run, the forces between atoms is not zero(only negligible), when i do the 2nd run, the atoms start moving under the action of these forces and since there is no temperature scaling or pressure scaling, we can or might see an increase in KE as