Re: NAMD pairInteraction - huge VDW and TOTAL3

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Dec 06 2006 - 21:21:32 CST

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
>>>
>>>
>
>

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