On 5/16/16 12:23 AM, Ms. Nikita Bora wrote:
---------------------------- Original Message ----------------------------
Subject: Re: simulation_time
From: "Ms. Nikita Bora" <nik...@tezu.ernet.in>
Date: Mon, May 16, 2016 9:42 am
To: nik...@tezu.ernet.in
--------------------------------------------------------------------------
Respected Sir,
Thanks for the reply. I would further like to know that according to this
tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
the rvdw=rcoulomb=1 is used for the protein while according to this
tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
and protein-ligand complex is used??
Different force fields, different settings.
-Justin
Respected Sir,
Recently i followed your tutorial for simulation of a 50 ns final mdrun
of protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used.
The simulation runned at aorund 10 ns/day . While for the same complex
when rvdw=rcoulomb=1 is made the run was 10 ns/day.
Sir i would like to know is there any standard value for rvdw,rcoulomb
and why a longer time is taken for 1.4 value
___________________
D I S C L A I M E R
This e-mail may contain privileged information and is intended solely
for the individual named. If you are not the named addressee you should
not disseminate, distribute or copy this e-mail. Please notify the
sender immediately by e-mail if you have received this e-mail in error
and destroy it from your system. Though considerable effort has been
made to deliver error free e-mail messages but it can not be guaranteed
to be secure
or error-free as information could be intercepted, corrupted, lost,
destroyed,
delayed, or may contain viruses. The recipient must verify the integrity of
this e-mail message.
___________________
D I S C L A I M E R
This e-mail may contain privileged information and is intended solely for
the individual named. If you are not the named addressee you should not
disseminate, distribute or copy this e-mail. Please notify the sender
immediately by e-mail if you have received this e-mail in error and
destroy it from your system. Though considerable effort has been made to
deliver error free e-mail messages but it can not be guaranteed to be
secure or error-free as information could be intercepted, corrupted,
lost, destroyed, delayed, or may contain viruses. The recipient must
verify the integrity of this e-mail message.
___________________
D I S C L A I M E R
This e-mail may contain privileged information and is intended solely for
the individual named. If you are not the named addressee you should not
disseminate, distribute or copy this e-mail. Please notify the sender
immediately by e-mail if you have received this e-mail in error and
destroy it from your system. Though considerable effort has been made to
deliver error free e-mail messages but it can not be guaranteed to be secure
or error-free as information could be intercepted, corrupted, lost, destroyed,
delayed, or may contain viruses. The recipient must verify the integrity of
this e-mail message.
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
