RE: mail about non bonded parameters

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Jun 13 2018 - 05:13:09 CDT

Hi,

Yes. Take a look at your parameter files. In standard CHARMM nonbonded parameter files, you've got a line something like this:

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5

This specifies a bunch of input parameters in CHARMM (the MD package, not the force field), which you are tasked to replicate as closely as possible. The full specification of what this means can be looked up in the CHARMM documentation (see https://www.charmm.org/charmm/documentation/by-version/c42b1/params/doc/nbonds/),>). These are the basic input arguments to put in for NAMD:

cutoff 12
switching on
vdwForceSwitching on
switchdist 10
exclude scaled1-4
1-4scaling 1.0

You will also need long range electrostatics taken care of, where the manual recommends something like:

PME on
PMEGridSpacing 1.0

-Josh

On 2018-06-11 20:07:52-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Dear Namd users
                         How to  Calculate   non-bonded energies such as  cut-offs, shifting, switching  etc.for my lipid protein system . Is there is any rule to evaluate ?      i am using charmm 36 force field . Otherwise is there is any standard value  for given charmm 36 force field

With regards
S.Vidhyasankar

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