Re: [gmx-users] recalculating .trr from .xtc

2013-10-15 Thread XAvier Periole
Interactions will be off, especially the bonded terms. On Oct 15, 2013, at 7:21, Mark Abraham mark.j.abra...@gmail.com wrote: Also, the precision was selected when the xtc file was written, ie in the mdp file. Mark On Oct 15, 2013 3:24 AM, Justin Lemkul jalem...@vt.edu wrote: On

Re: [gmx-users] Number of ligand contacts over the trajectories

2013-10-15 Thread anu chandra
Thanks a lot for reply. On Mon, Oct 14, 2013 at 12:34 PM, bipin singh bipinel...@gmail.com wrote: g_mindist with -on and -d option. On Mon, Oct 14, 2013 at 11:37 AM, anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I am working with protein-ligand interaction. I would like

Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)

2013-10-15 Thread Mark Abraham
On Thu, Oct 10, 2013 at 2:34 PM, James jamesresearch...@gmail.com wrote: Dear Mark, Thanks again for your response. Many of the regression tests seem to have passed: All 16 simple tests PASSED All 19 complex tests PASSED All 142 kernel tests PASSED All 9 freeenergy tests PASSED All 0

[gmx-users] topology file of ligand

2013-10-15 Thread sunyeping
Dear gromacs users,   I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he  immediately notice three things that are wrong with this topology, which include

Re: [gmx-users] topology file of ligand

2013-10-15 Thread Justin Lemkul
On 10/15/13 11:24 AM, sunyeping wrote: Dear gromacs users, I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the topology file. The author state that he immediately notice three things that

答复: [gmx-users] topology file of ligand

2013-10-15 Thread sunyeping
Thank you Dr. Lemkul,   Could you recommand some primary literatures which are most usefule for me to understand the force field?  Yeping Sun Institute of Microbiology, Chinese Academy of Sciences --发件人：Justin Lemkul

Re: 答复: [gmx-users] topology file of ligand

2013-10-15 Thread Justin Lemkul
On 10/15/13 12:25 PM, sunyeping wrote: Thank you Dr. Lemkul, Could you recommand some primary literatures which are most usefule for me to understand the force field? The ones cited in the Gromacs manual are a good start. One should never attempt to use a force field without