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
<ndhu...@andrew.cmu.edu>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. How can I take
average over 128 ion pairs and save snap shot for a single ion pair.
I don't understand the average mean here?
if you wanna get the average.pdb in some time interval try g_rmsf -ox -b
-e
you may wait for some other better answers.
Basically I want to use classical md geometry for quatum chemical
calculation.
I am using Gromacs 4.0.7 version.
Thanks
Nilesh
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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