Re: [gmx-users] Long bond streches during simulations

2014-10-29 Thread Dr. Vitaly Chaban
It is disgusting that the bond dares to stretch... Perhaps, there is no harmonic bond record for this bond in the topology? Would you like to provide numbers characterizing this long stretch, perhaps? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Wed, Oct 29, 2014 at 11:21 AM, Seera Suryan

Re: [gmx-users] Long bond streches during simulations

2014-10-29 Thread Justin Lemkul
On 10/29/14 6:21 AM, Seera Suryanarayana wrote: Dear gromacs users I have done mdrun upto 50ns by using the command "gmx mdrun -deffnm md_0_1 -nt 7. I have total 8 threads and I used 7 out of it along with graphic card nvidia tesla 2075. I first thing I would like to know that when I load th

[gmx-users] Long bond streches during simulations

2014-10-29 Thread Seera Suryanarayana
Dear gromacs users I have done mdrun upto 50ns by using the command "gmx mdrun -deffnm md_0_1 -nt 7. I have total 8 threads and I used 7 out of it along with graphic card nvidia tesla 2075. I first thing I would like to know that when I load the .trr or .xtc file after the .gro file into the vmd