Re: [gmx-users] snap shot

2011-10-10 Thread Justin A. Lemkul
Nilesh Dhumal wrote: Hello, How can I save the coordinates (in pdb or xyz format) for a particular snap shot. trjconv -dump -Justin Nilesh On Sat, October 8, 2011 10:06 am, lina wrote: On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal wrote: Hello, I have a system with 128 emi (catio

Re: [gmx-users] snap shot

2011-10-10 Thread Nilesh Dhumal
Hello, How can I save the coordinates (in pdb or xyz format) for a particular snap shot. Nilesh On Sat, October 8, 2011 10:06 am, lina wrote: > On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal > wrote: > > >> Hello, >> >> >> I have a system with 128 emi (cations) and 128 Cl (anions). I run the >>

Re: [gmx-users] snap shot

2011-10-10 Thread Mark Abraham
On 8/10/2011 5:21 AM, Nilesh Dhumal wrote: Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I run the simulation for 20 ns. I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. So you need a suitable combination of nstxout and post-processing with trjconv. I don't want

Re: [gmx-users] snap shot

2011-10-10 Thread lina
On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal wrote: > Hello, > > I have a system with 128 emi (cations) and 128 Cl (anions). I run the > simulation for 20 ns. > > I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. > trjconv use -dt 5000 > > I don't want to save snap shot for 128 ion-pairs. H

[gmx-users] snap shot

2011-10-07 Thread Nilesh Dhumal
Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I run the simulation for 20 ns. I want to save snap-shot at 5ns, 10ns, 15ns and 20ns. I don't want to save snap shot for 128 ion-pairs. How can I take average over 128 ion pairs and save snap shot for a single ion pair. Basicall