[gmx-users] Fwd: MD simulation using TFE

[Justin Lemkul]

On 8/14/15 4:50 AM, Bikash Ranjan Sahoo wrote:
>
> Dear Dr. Justin,
>
> Thank you so much for your time and kind reply.
>
> I have used maxwarn as there is fatal error due to large rlist.
> *The sum of the two largest charge group radii (23.903836) is larger than*
> *  rlist (1.000000)*
> *
> *
> I do not exactly understand this point.**

It suggests something is wrong with the topology, coordinates, or both.

http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

> *Don't try to simultaneously add a box of solvent and do random insertions of
> molecules.  This is one of the reasons that genbox was split into two different
> programs in recent versions; people make this mistake too often.**
> *
> *
> *
> Kindly guide me how to generate the initial box.
>
> Please help in finding the exact command in genbox to create the initial
> Water+TFE complex (will be grateful to you if you will write the command here)
>

I've posted about this exact thing (even using TFE!) in recent days.  Pay 
attention to other messages on the list.  TFE solvation seems to be the most 
popular topic in recent days.

The exact process is described in:

http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

-Justin

-- 
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================