Hi,
Note that you can also use the cpptraj command 'setvelocity' to set
random velocities for your output restart file. See the manual for
full details.
-Dan
On Mon, Jan 29, 2018 at 2:57 PM, David A Case <david.case.rutgers.edu> wrote:
> On Mon, Jan 29, 2018, Khabiri, Morteza wrote:
>>
>> I have an equilibrated DNA system. I have generated a point mutation
>> in my equilibrated DNA system and want to run mutant DNA for
>> sometimes. However, except for the atoms in mutated nucleotide(nt),
>> I want to use the velocity from my output wildtype DNA system
>> (restartfile) as an initial velocity for the rest of the atoms in my
>> mutated DNA system. For the atoms in mutated nt, I am going to generate
>> velocity based on maxwell-Bultmann distribution. Is there any way that
>> I can extract the velocity for all atoms except perturbed one from
>> wildtype system, and use it as an initial velocity for the atoms in
>> mutated system?
>
> You can get the velocities of the original system from one of it's restart
> files. Then, with some hand-editing (use formatted restarts) you could put
> those values into a new restart file for the mutated system.
>
> But this seems like a lot of work for zero gain. If you are using Maxwell
> Boltzmann initial velocities for some atoms, I don't immediately see any good
> argument for not using randomized velocities for all atoms.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 01 2018 - 06:30:03 PST
