[gmx-users] changing the time frame for simmulation
jalemkul at vt.edu
Thu Apr 12 19:35:28 CEST 2018
On 4/12/18 1:33 PM, neelam wafa wrote:
> Thank you sir justin.
> I am confused a bit. Kindly tell me which one of the following is right for
> 5 ns.
> nsteps =5000000; 5000000=5000 ps (5ns)
> nsteps = 2500000 ; 2*2500000= 5000 ps (5ns).
Depends on dt. Please consider what the units are. This is a trivial
calculation and is actually explained exactly in the comment field of
the file you posted previously (and in the tutorial from which you got
> On Thu, 12 Apr 2018 10:13 pm Justin Lemkul, <jalemkul at vt.edu> wrote:
>> On 4/12/18 4:11 AM, neelam wafa wrote:
>>> Dear gmx users,
>>> I have run the md simmulation of my protein ligand complex for 1ns
>>> following the conditions used in tutorial by sir Justin. Now I want to
>>> the simmulations for 5ns and 10 ns. How have set it like this:
>>> integrator = md ; leap-frog integrator
>>> nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)
>>> dt = 0.002 ; 2 fs
>>> Is it right?
>>> Is it needed to change the output control as well. It is in this form
>>> Output control
>>> nstxout = 0 ; suppress .trr output
>>> nstvout = 0 ; suppress .trr output
>>> nstenergy = 5000 ; save energies every 10.0 ps
>>> nstlog = 5000 ; update log file every 10.0 ps
>>> nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps
>>> Please also guide me is it enough to run the last production md for 10 ns
>>> with the npt and nvt run unchanged or I have change the time frame of the
>>> equliberation steps as well.
>> You do not need to change the amount of equilibration.
>>> Further how can I set the parameters for a 5ns simmulation?
>> It's the same math that you did above.
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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