# Re: Free energy calculation using MM-GBSA with NAMD

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Jun 15 2016 - 09:10:21 CDT

Hi Sneha,

The ELECT column of the NAMD log file contains the total electrostatic
contribution including ∆G(solv).

Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

On Wed, Jun 15, 2016 at 12:50 PM, Sneha Menon <sneha.menon15_at_gmail.com> wrote:
> Dear NAMD community,
>
> We are trying to calculate the solvation free energy as well as binding free
> energy, of a protein-carbon nanotube (CNT) system using MM-GBSA (single
> trajectory) method.
>
> We followed a post in NAMD mailing list regarding a similar system, link
> given below:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2726.html
>
> It is mentioned in the post that the potential energy obtained from the
> MM-GBSA log file is the GBSA free energy. As we know, the free energy of a
> system is given by:
>
> ∆G = ∆E(internal) + ∆E(vdw) + ∆E(ele) + ∆G(solv)
>
>
> So if we consider the potential energy as the GBSA free energy; ∆G will be
> equal to [ ∆E(internal) + ∆E(vdw) + ∆E(ele)]. Hence, ∆G(solv) will become
> zero. Is our understanding wrong here?
>
> On a different note, for our protein-CNT system, MMGBSA calculation for only
> the CNT does not yield zero for the electrostatic contribution ∆E(ele) (CNT
> does not carry any charge). What could be the reason?
>
> Our input file for only CNT system is as follows:
>
> coordinates nt.pdb
> structure nt.psf
> paraTypeCharmm on
> parameters par_all22_prot_cmap.inp
> outputname gb_nt
> numsteps 0
>
> GBIS on
> solventDielectric 74.69
> ionConcentration 0.3
> alphaCutoff 14
> switching on
> switchdist 15
> cutoff 16
> pairlistdist 18
> sasa on
> surfaceTension 0.0072
> timestep 1
> nonbondedFreq 2
> fullElectFrequency 4
> exclude scaled 1-4
> temperature 310
>
> set ts 0
>
> coorfile open ____.dcd
> while { ![coorfile read] } {
> firstTimestep \$ts
> run 0
> incr ts 1
> }
> coorfile close
>
> Any help would be appreciated.
>
> Regards,
> Sneha

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