Re: NAMD pairInteraction - huge VDW and TOTAL3

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Dec 06 2006 - 19:44:07 CST

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
>

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