[gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

[Justin Lemkul]

On 6/20/16 12:04 PM, Dan Gil wrote:
> Hi Mark,
>
> I thought about your said, and tried to manage the VDW radi of atoms with
> the "-radius" option.
> I believe it scales the known VDW radi values by the number specified by
> me. So I try:
> "gmx insert-molecules ... ... -radius 1.2"
>
>  The result is still the same, I get segmentation errors because rms goes
> to nan. I try again with "-radius 1.5" and I am still getting lucky.
>

Your interpretation is incorrect.  See the help information, which explains:

"A database (vdwradii.dat) of van der Waals
radii is read by the program, and the resulting radii scaled by -scale. If
radii are not found in the database, thoseatoms are assigned the (pre-scaled)
distance -radius."

Setting radii that large (over 1 nm) will probably make it hard for anything but 
the first few molecules to be inserted at all.

-Justin

> Also, excuse me for creating a new question again. I was subscribed to
> receive batch emails from the users-list, and I did not know how to respond
> questions in that mode.
>
> Thanks,
>
> Dan
>

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

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

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