[gmx-users] genconf -trj?!?

stion"http://lists.gromacs.org/pipermail/gmx-users/2004-July/011196.html"; whithout answer. Please guide me wheather this command can help me to generate an aggregated system for analyzing? If Yes, How? If No help me please?Thank you in advance Faezeh Kargar -- This message has been scanned for v

[gmx-users] top2psf.pl

Dear All, I used top2psf.pl to visualize bonds in my coarse grained simulation with MARTINI ff. it worked well. my system contained a box of 1 protein and several hundreds of water molecules. then I repeated the box to make a bigger system with command below: genconf -nbox 2 2 2 -f 1box.gro -o

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

Thank you very much for your reply. could you please tell me if there is any way to solve this problem and restart running the code? Karagr > On 30/04/2011 11:37 PM, Faezeh Kargar wrote: >> >> >> > On 4/30/2011 7:22 PM, Faezeh Kargar wrote: >> >> >&

Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

> On 4/30/2011 7:22 PM, Faezeh Kargar wrote: >> >> Dear gmx users, >> >> My code stops running because of electricity voltage oscillation. it >> happened for several times and each time I restarted running my code. >> but for this time w

[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4

×M5~Ë­­ªyïxã]¹ß]7ãMuÓ Program mdrun, VERSION 4.0.7Source code file: checkpoint.c, line: 565Fatal error:Attempting to read a checkpoint file of version 12 with code of version 4-- 83_kargar-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clea

[gmx-users] Warning: atom names in CG topology file and CG pdb file do not match

Dear All I searched my problem in users mailing list but I could not find the answer. please help me with this. I am learning the CG Martini force filed using the tutorial "protein in water" for protein ubiquitin. so I did the things like below: 1. awk -f atom2cg_v2.1.awk 1UBQ.pdb > 1UBQ-cg

Re: [gmx-users] coarse grainig with Martini ff???

Dear Justin Thank you for your reply. this simulation contains a peptide and water in a specified pH. Do you think this .pdb file is correct. Thank you Kargar > > > Faezeh Kargar wrote: >> Dear All >> >> I asked this question in Martini's forum, but tile no

[gmx-users] coarse grainig with Martini ff???

ßÞ7~Ë­­ª}ëÏxç^xÓnöÛ]5Ó Dear All I asked this question in Martini's forum, but tile now no answer, so I had to ask it here. excuse me.I did an atomistic peptide simulation. The residues and positions of all atoms in this peptide created by my self, I mean I didn't download the pdb file from . at th