From: Ravinder Abrol (abrol_at_wag.caltech.edu)
Date: Thu Dec 07 2006 - 03:23:58 CST
Hey Peter.
NAMD 2.6 solved the problem. Now dcd or pdb input give identical
interaction energy output using pairInteraction.
Thanks very much,
Ravi
-------------------------------------------
On Wed, 6 Dec 2006, Peter Freddolino wrote:
> Hi Ravi,
> as a first step, please try again with NAMD 2.6 and make sure you're
> using periodic boundary conditions (available through the VMD interface
> in VMD >= 1.8.5). NAMD2.5 did not have some necessary code for using PME
> and periodic dcds with pairinteractions.
> Peter
>
> Ravinder Abrol wrote:
> > 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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