[gmx-users] Re: change in secondary structure

bharat gupta bharat.85.monu at gmail.com
Wed Feb 2 14:39:06 CET 2011


Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1
will eventually lead to different simulation and thus different simulated
structures ?? .. and after completing one set of simulation with this
paramter and 3ns time .. do i have to repeat it some 3 or more times ??....
pls comment.. as  I am going to start simulation with these parameters.

On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> bharat gupta wrote:
>
>> Thanks for such a detailed reply to my queries .. But conducting a 50ns
>> simulation will take time ... so i want to conduct independent simulation
>> and for that I searched some threads but was not able to get the proper
>> description and method... if u can guide me through an appropriate link ..
>> it would be much more helpful ..
>>
>
> Each simulation begins with the assignment of random velocities (gen_vel =
> yes).  Specify different values of gen_seed (or leave it set to -1) to get
> different velocities each time.
>
> -Justin
>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110202/23ea452c/attachment.html>


More information about the gromacs.org_gmx-users mailing list