From: Ravinder Abrol (abrol_at_wag.caltech.edu)
Date: Wed Dec 06 2006 - 20:35:15 CST
Hi Peter,
I am using NAMD 2.5 for Linux-i686. I had similar problems with my NPT
generated dcd files.
I loaded a single pdb file and it fixed the large TOTAL3 as well as large
VDW problems. Is there a way to load multiple pdb files or a concatenated
pdb file in the NAMD configuration file because coorfile works only with
dcd files? This will help me get interaction energies along a trajectory.
There seems to be a problem with dcd files and pairInteraction. If I load
a single frame dcd, the large value (99999999.9999) problem goes away for
both VDW and TOTAL3, but the energies are not physical. They appear to
be reasonable when I load the same frame in pdb format (e.g., the
interaction energies between i,i+4 residues on a helix are around
-18 (ELEC) and 54 (VDW) kcal/mol with a dcd snapshot input, compared to
-1.11 (ELEC) and -1.10 (VDW) kcal/mol with a pdb snapshot). Let me know if
you need my input/output files, I will be happy to send them.
Thanks very much,
Ravi
-------------------------------------------
On Wed, 6 Dec 2006, Peter Freddolino wrote:
> Hi Ravi,
> could you please let me know what version of NAMD you're using? Also,
> I've heard of some unusual behavior that can happen when you use pair
> interactions with a constant volume dcd. You may want to write a pdb of
> a single frame and see if the bad behavior still occurs. I know this is
> currently being looked at.
> Peter
>
> Ravinder Abrol wrote:
> > Dear All,
> > I am trying to use pairInteraction option of NAMD on a trajectory output
> > from an NVE run and was trying to follow the interaction between a pair of
> > residues in my protein which is embedded in a membrane.
> >
> > The configuration file is included at the end of this email for reference.
> > I am getting huge VDW and TOTAL3 energies for some snapshots and it
> > doesn't make sense because the log from the original NVE run didn't show
> > this behavior. Besides, the protein-lipid system has been well
> > equilibrated for many nanoseconds.
> >
> > Here is an example output for interaction energies for some snapshots that
> > shows the range of answers I am getting:
> >
> > ETITLE: TS BOND ANGLE DIHED IMPRP
> > ELECT VDW BOUNDARY MISC KINETIC
> > TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
> >
> > ENERGY: 1000 0.0000 0.0000 0.0000 0.0000
> > 0.0060 -0.0000 0.0000 0.0000 0.0000
> > 0.0060 0.0000 0.0060 0.0060 0.0000
> >
> > ENERGY: 2000 0.0000 0.0000 0.0000 0.0000
> > -331.7372 99999999.9999 0.0000 0.0000 0.0000
> > 99999999.9999 0.0000 99999999.9999 -99999999.9999 0.0000
> >
> > ENERGY: 5000 0.0000 0.0000 0.0000 0.0000
> > 29.4931 1.7362 0.0000 0.0000 0.0000
> > 31.2293 0.0000 31.2305 99999999.9999 0.0000
> >
> > ENERGY: 49000 0.0000 0.0000 0.0000 0.0000
> > 0.0000 0.0000 0.0000 0.0000 0.0000
> > 0.0000 0.0000 0.0000 99999999.9999 0.0000
> >
> > ENERGY: 59000 0.0000 0.0000 0.0000 0.0000
> > -17.7699 53.6117 0.0000 0.0000 0.0000
> > 35.8417 0.0000 36.0596 99999999.9999 0.0000
> >
> > ENERGY: 62000 0.0000 0.0000 0.0000 0.0000
> > 215.7875 99999999.9999 0.0000 0.0000 0.0000
> > 99999999.9999 0.0000 99999999.9999 -99999999.9999 0.0000
> >
> > As you can see, sometimes TOTAL3 by itself is large and positive and at
> > other times when VDW is huge, TOTAL3 becomes a large negative number.
> > There are no bad VDW contacts in this well equilibrated system.
> >
> > The configuration file for interaction energy calculation looks like:
> >
> > #--------------------------------------------------------------------------
> > # interaction config
> > coordinates interaction2.pdb
> > temperature 0
> >
> > # output params
> > outputname hccr1_apo_analyze
> > binaryoutput no
> >
> > # integrator params
> > timestep 1.0
> >
> > # force field params
> > paratypecharmm on
> > structure ../Rapo+POPC+wat+Cl.psf
> > parameters par_all22_prot.inp
> > parameters par_all27_lipid.inp
> > exclude scaled1-4
> > 1-4scaling 1.0
> > switching on
> > switchdist 10.0
> > cutoff 12.0
> > pairlistdist 13.5
> > stepspercycle 20
> >
> > # Atoms in group 1 have a 1 in the B column; group 2 has a 2.
> > pairInteraction on
> > pairInteractionFile interaction2.pdb
> > pairInteractionCol B
> > pairInteractionGroup1 1
> > pairInteractionGroup2 2
> >
> > # First frame saved was frame 1000.
> > set ts 1000
> > coorfile open dcd eq02_stride100.dcd
> >
> > # Read all frames until nonzero is returned.
> > while { ![coorfile read] } {
> >
> > # Set firstTimestep so our energy output has the correct TS.
> > firstTimestep $ts
> >
> > # Compute energies and forces, but don.t try to move the atoms.
> > run 0
> > incr ts 1000
> > }
> > coorfile close
> > #---------------------------------------------------------------
> >
> > Any help is appreciated to resolve the large VDW and large TOTAL3
> > problems.
> >
> > Thanks very much,
> > Ravi
> >
>
-- ________________________________________________ Ravinder Abrol 139-74, Beckman Institute Division of Chemistry and Chemical Engineering Caltech, Pasadena, CA 91125 Phone: 1.626.395.8143 Fax: 1.626.585.0917 Email: abrol_at_wag.caltech.edu ________________________________________________
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