Re: [gmx-users] Question about make_ndx and g_angle

Dear Changwoon, why are you using ./make_ndx instead of make_ndx? Did you try to use the command without ./? Regards El jue, 07-11-2013 a las 14:12 -0800, Chang Woon Jang escribió: > Dear Users, > > I am using openSUSE 12.3 and try to use make_ndx and g_angle. When I try > the following com

Re: [gmx-users] extra gro file generation

Dear Sarah, you have to use the trjconv command with the flags -b -e and -sep. For example: trjconv -f xxx.trr -s xxx.tpr -o out.gro -b (initial frame to read in ps) -e (last frame to read in ps) -sep Regards El mar, 05-11-2013 a las 01:04 -0800, sarah k escribió: > Dear all, > > I'm going to perf

Re: [gmx-users] No group in index file?

Dear Xu, you have to use the make_ndx option if I'm not wrong. The syntax should be make_ndx -f xxx.gro -o index.ndx Cheers, -Original Message- From: Xu Dong Huang Sent: Thursday, October 31, 2013 8:52 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] No group in index f

Re: [gmx-users] problem vwith ethanol-water solution

Dear Ehsan, Did you try to pack your box with packmol? I have a similar system and packmol pack my system quite well and in a random way. Regards, Riccardo -Original Message- From: Ehsan Sadeghi Sent: Thursday, October 31, 2013 7:25 PM To: Discussion list for GROMACS users Subject: [g

Re: [gmx-users] cool down problem

:25 AM, Riccardo Concu wrote: > > Dear all, I'm having some problems during the cool-down process after > > the NVT. > > I'm running the NVT process at a T of 500K for 3ns and everything is > > going well but when I cool down the system blows up. I am running the >

[gmx-users] cool down problem

Dear all, I'm having some problems during the cool-down process after the NVT. I'm running the NVT process at a T of 500K for 3ns and everything is going well but when I cool down the system blows up. I am running the cool down for 100ps, I tried to run the process for longer time (500 ps) and dec