From: Kasam, Vinod (vkasam_at_coh.org)
Date: Thu Sep 13 2012 - 13:12:24 CDT
Hi Chris
The difference is only little, for instance the RMSD is 0.003 for ~200Residue protein.
Here are the final energy difference after the 1000 steps of the minimization (end of the log file):
ETITLE: TS BOND ANGLE DIHED | ETITLE: TS BOND ANGLE DIHED
ENERGY: 1000 104.0472 340.7871 413.4311 | ENERGY: 1000 103.8107 339.5444 413.5337
It is only slightly different, however, as I have to calculate the ddG of complex to a mutant, the small differences are sensitive for the final analysis.
Thank you,
Vinod
________________________________________
From: Chris Harrison [charris5_at_gmail.com]
Sent: Thursday, September 13, 2012 9:50 AM
To: Kasam, Vinod
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Unable to reproduce same results in minimization with GBIS
Vinod,
"Kasam, Vinod" <vkasam_at_coh.org> writes:
> I am running a minimizationin NAMD using the parameters shown below. When I ran minimization using the same parameters in two different folders with the same input (protein), I am ending up in different results.
> The co-ordinates of the proteins and the energy values after minimization are different.
How different? Please attempt to quantitate it? ie, rmsd plots,
energy difference plot, etc.
Chris
> However, if I do not use GBIS (comment out GBIS input parameters), the results are same and just FINE.
>
> I am new to NAMD and I am using NAMD2.8 version, can some explain me why are the results different for the same input if I use GBIS.
>
> Thank you,
> Vinod
>
>
>
>
> # MOLECULAR SYSTEM
> structure min_WT-chain_D.psf
> coordinates min_WT-chain_D.pdb
>
>
> # FORCE FIELD
> paraTypeCharmm on
> parameters par_all22_prot_cmap.inp
>
>
> # APPROXIMATIONS
> switching on
> switchdist 15
> cutoff 16
> pairlistdist 17.5
> #margin 3
> exclude scaled1-4
> 1-4scaling 1.0
> dielectric 3
> seed 20111012
>
> #INTEGRATOR
> timestep 1.0
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
>
> #GBIS - Implicit solvent
> GBIS on
> solventDielectric 78.5
> ionConcentration 0.2
> alphaCutoff 15
>
>
> # PERIODIC BOUNDARY CONDITIONS
> cellBasisVector1 51.76400065422058 0 0
> cellBasisVector2 0 45.07099914550781 0
> cellBasisVector3 0 0 43.320000648498535
> cellOrigin 28.250900268554688 39.77300262451172 7.405788421630859
>
>
> # WRAPPING
> wrapAll on
>
>
>
> # OUTPUT
> outputname monomerA-crystal-min
> dcdfreq 500
> xstfreq 10000
>
> outputenergies 10
> outputtiming 100
> binaryoutput no
> binaryrestart yes
>
>
> # RESTART FILES
> restartname res
> restartfreq 1000
> restartsave yes
>
>
> # TEMPERATURE CONTROL
> temperature 0
>
>
> minimize 1000
>
>
>
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Best,
Chris
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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