From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Jul 30 2018 - 09:09:24 CDT
Dear Vidhya
,
The issue should not be in the simulation but in the psf and pdb files.
Please make sure that the psf file that you are using the autoionize plugin
correspond to the system in the pdb file, and no other change was made to
the pdb and psf, beside modifications in the atoms' coordinates.
Best
João
On Sat, Jul 28, 2018 at 1:24 AM Vidhya Sankar <
vidhyasankar7928_at_remove_yahoo.com> wrote:
> Thank you João Ribeiro sir,
> I am doing equilibration dynamics (protein/Membrane
> system) for protein kept above Membrane while protein is kept fixed during
> my equilibration . i ran dynamics without adding ions but later on i
> needed to add ions then wish to run my equilibration dynamics
> i have used the following force field parameter and other parameter in my
> .conf files
>
>
> paraTypeCharmm on
> parameters /home/others/ponkvel/namdsvs/dwe/par_all36_lipid.prm
> parameters /home/others/ponkvel/namdsvs/dwe/par_all36_lipid.prm
> parameters /home/others/ponkvel/namdsvs/dwe/par_all36_prot.prm
> parameters
> /home/others/ponkvel/namdsvs/dwe/toppar_water_ions_namd1.str
> parameters /home/others/ponkvel/namdsvs/dwe/par_all36_carb.prm
> parameters
> /home/others/ponkvel/namdsvs/dwe/par_all36_cgenff.prm
>
> wrapWater on
> wrapAll on
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 25
> switching on
> switchdist 10.
> pairlistdist 25
>
> constraints on
> consexp 2
> constraintScaling 1
> consref /home/others/ponkvel/namdsvs/newtutmem2.pdb
> conskfile /home/others/ponkvel/namdsvs/proteinconstrainedM.cnst
> conskcol B
> margin 3
> # selectConstraints on
> # selectConstrZ on
> fixedAtoms on
> fixedAtomsForces off
> fixedAtomsFile /home/others/ponkvel/namdsvs/proteinconstrainedM.cnst
> fixedAtomsCol B
> tclforces on
> set waterCheckFreq 100
> set lipidCheckFreq 100
> set allatompdb
> /home/others/ponkvel/namdsvs/newtutmem2.pdb
> tclForcesScript
> /home/others/ponkvel/namdsvs/keep_water_out.tcl
>
> # eFieldOn yes
> # eField 0 0 -0.155
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {1} {
> minimize 100000
> reinitvels 100
> }
>
> run 2500000 ;# 0.5 ns
>
>
> with high regards and respect
> S.Vidhyasankar
>
>
>
>
>
>
-- ……………………………………………………... João Vieira Ribeiro Theoretical and Computational Biophysics Group Beckman Institute, University of Illinois http://www.ks.uiuc.edu/~jribeiro/ jribeiro_at_ks.uiuc.edu +1 (217) 3005851
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