[gmx-users] About Grid MAT

Justin Lemkul jalemkul at vt.edu
Thu Jan 17 17:00:07 CET 2013

On 1/17/13 10:56 AM, vidhya sankar wrote:
> Dear  Justin Thank you for your Previous Reply Mail
>                        I am using GridMAt MD Script When I run the APL Headgroup Calculation It runs well But  I Have got  Output With  the Following Comment in My Command Prompt
> looking for offending protein atoms...
> There are 143 protein atoms within the headgroups of the top leaflet
> There are 65 protein atoms within the headgroups of the bottom leaflet
> To Avoid this Which Parameter Should I adjust Either precision   Parameter or  P_value     Parameter

This is the correct output.  If you are doing an APL calculation in the presence 
of a protein, that needs to be taken into account.

You can send GridMAT-MD questions directly to me rather than spamming the list 
with non-Gromacs questions.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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