From: Jun Zhang (coolrainbow_at_yahoo.cn)
Date: Sun Apr 18 2010 - 03:21:38 CDT
Hi Chipot:
Thank you for your reply. I apologize that I have forgotten to sign my name. I am a graduate in chemistry and my main interest is biophysics. I just began to study NAMD for 3 months, now I am planning to perform FEP calculation so start to study it.
Unfortunately, I have checked my psf generated by alchemify but I have not found anything wrong:
alchemify setup.psf sodium.psf setup.fep
>WARNING: END keyword not found at the end of FEP file setup.fep
>
>FEPfile : 20525 atoms found, 1 initial, 1 final.
>
>6841 angles : removing 0 angles coupling initial and final groups
>0 dihedrals
>0 impropers
>Writing 1 exclusion pairs
There does exist one exclustion pairs. Maybe the "WARNING" means my fep file is wrong? My fep is :
>REMARK original generated coordinate pdb file
>ATOM 1 SOD SOD 1 0.000 0.000 0.000 1.00 1.00 NA0 NA
>ATOM 2 NA0 NA0 2 0.000 0.000 0.000 1.00 -1.00 NA0 NA
>ATOM 3 OH2 TIP3 3 -17.244 23.344 -26.144 1.00 0.00 WT1 O
>ATOM 4 H1 TIP3 3 -17.473 23.366 -25.167 1.00 0.00 WT1 H
>ATOM 5 H2 TIP3 3 -17.961 23.747 -26.546 1.00 0.00 WT1 H
..
>ATOM 20525 H2 TIP3 9260 26.177 -28.807 19.574 1.00 0.00 WT1 H
>END
The nnb part of my psf file is:
> 1 !NNB
> 1
> 0 1 1 1 1 1 1 1
> 1 1 1 1 1 1 1 1
> 1 1 1 1 1 1 1 1
> 1 1 1 1 1 1 1 1
> 1 1 1 1 1 1 1 1
....
> 1 1 1 1 1 1 1 1
> 1 1 1 1 1
>
> 1 0 !NGRP
> 0 0 0
Is there anything wrong? I really don't know. The md dies again :
>PRESSURE: 0 nan nan nan nan nan nan nan nan nan
>GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
>ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>ENERGY: 0 0.0000 0.0000 0.0000 0.0000 -50748.1715 9999999999.9999 0.0000 0.0000 nan nan nan 9999999999.9999 nan nan nan nan 27000.0000 nan nan
>OPENING FEP ENERGY OUTPUT FILE
>OPENING EXTENDED SYSTEM TRAJECTORY FILE
I am really confused. Thanks a lot.
Jun Zhang
Jun Zhang
Nankai University
coolrainbow_at_yahoo.cn
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