On 2/21/13 12:33 AM, bipin singh wrote:
Hello All,
I want to know how to mention a group (group2) without any temperature
coupling in mdp file. From the manual I got to know that we should mention
tau_t= -1 for no temperature coupling. And in the ref_temp section I have
mention two values, 300K for coupled part (group1) and 10k for uncoupled
part (group2). But my doubt is while generating velocities, which
temperature I should mention in gen_temp section (i.e. 300K or 10K),
because as far as I know we can not mention two different temperatures in
gen_temp section while generating velocities. But ideally I want the
uncoupled part to be at 10K and coupled part at 300K at the starting.
Please let me know, which of the below scheme is correct for this purpose:
* Method:1*
Tcoupl= V-rescale
tau_t= 0.1 -1
tc_grps= group1 group2
ref_t= 300 10
gen_vel= yes
gen_temp= 300
*Method:2*
Tcoupl= V-rescale
tau_t= 0.1 -1
tc_grps= group1 group2
ref_t= 300 10
gen_vel= yes
gen_temp= 10
I don't really see what difference it makes if the group is not actually
regulated by the thermostat. If it's not subjected to temperature coupling, you
can't keep it at 10 K.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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