[gmx-users] simulation_time

[Ms. Nikita Bora]

---------------------------- Original Message ----------------------------
Subject: Re: simulation_time
From:    "Ms. Nikita Bora" <niki24 at tezu.ernet.in>
Date:    Mon, May 16, 2016 9:42 am
To:      niki24 at 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??


> 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.