From: Lan Hua (lan.hua_at_gmail.com)
Date: Tue Nov 30 2010 - 16:04:52 CST
Thanks for your reply. My .xsc file was generated in GUI. From the
content as follows, it seems that PBCs should be enabled.
# NAMD extended system configuration file
# Generated by NAMDEnergy
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
0 77.20768356323242 0 0 0 77.0706901550293 0 0 0 77.19868469238281
12.847615242004395 -25.9986629486084 -3.900850296020508
Another thing still confused me is that whether the interactions between
(resid 100 and water) and its images have been included in the calculation.
Thank you very much!
On Tue, Nov 30, 2010 at 12:06 PM, Michael S. Sellers (Cont, ARL/WMRD) <
> XSC file (-extsys FILE): Use the specified xsc file to set up a periodic
> If your .xsc file was generated with PBCs enabled, then PBCs will be used
> in the VMD calculation.
> Lan Hua wrote:
>> Dear NAMD users,
>> I am wondering if the periodic boundary conditions have been applied
>> in the following calculation of interaction energy using namdenergy plugin
>> in VMD. It was done in text interface. The two atom selections are:
>> set sel1 [atomselect top "resid 100 and water"]
>> set sel2 [atomselect top "not (resid 100 and water)"]
>> The main options I specified are:
>> -elec -vdw -sel $sel1 $sel2 -cutoff 12 -switch 10 -extsys *.xsc
>> I want to know whether the obtained vmd energy and the electrostatic
>> energy (with pme (-pme), or without) were calculated under the periodic
>> boundary conditions. Are the interactions between (resid 100 and water) and
>> its images included in the calculation?
>> Thank you very much!!!
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