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

[Dan Gil]

You are right!

Thank you.

On Mon, Jun 20, 2016 at 1:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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