Re: Error in the Continuation TMD simulation Run.

From: Lutimba Stuart (lutimba.stuart_at_scilifelab.se)
Date: Wed Feb 21 2018 - 13:49:36 CST

Dear all

When running targeted MD simulations of a substrate entering into a
membrane protein binding pocket the substrate reaches its final destination
in a few ns although the total simulation time is 100ns, The issue is that
the RMSD distance does not evolve linearly in the specified time.

MY other issue is the continuation of from the last step when running TMD,
to make a total of 100ns, and to easily queue in my jobs at the cluster, i
have been creating dependencies but the sugar reaches its binding pocket in
the first 4 ns so on continuation from the last step in order to make
100ns, NAMD just runs the ordinary equilibration since the sugar is already
at the binding site, Am not sure if am running this in the right way, Am
grateful for any assistance and attached please is the configuration file
that am using.

####################################################################

set infile lac-TMD06

set outfile lac-TMD07

timestep 1.0

numsteps 10000000

structure occl_E325+H.psf

paraTypeCharmm on

parameters toppar_water_ions.str

parameters par_all36_prot.prm

parameters par_all36_lipid.prm

parameters par_all27_prot_lipid.prm

parameters par_all36_carb.prm

coordinates occl_E325+H.pdb

bincoordinates ${infile}.coor

binvelocities ${infile}.vel

outputname ${outfile}

outputEnergies 10000

outputTiming 10000

#outputPressure 100

#minimization on

stepspercycle 20

rigidBonds all

fullElectFrequency 4

nonbondedFreq 2

exclude scaled1-4

1-4scaling 1.0

switching on

vdwForceSwitching yes

switchdist 10.0

cutoff 12.0

pairlistdist 13.5

#set temperature 310

#temperature $temperature

extendedSystem ${infile}.xsc

#cellBasisVector1 105 0.0 0.0

#cellBasisVector2 0.0 108 0.0

#cellBasisVector3 0.0 0.0 85

cellOrigin -0.02 0.02 0.03

restartname ${outfile}

restartfreq 10000

DCDfile ${outfile}.dcd

DCDfreq 10000

DCDUnitCell yes

XSTfile ${outfile}.xst

XSTfreq 10000

PME on

PMEGridSizeX 140

PMEGridSizeY 140

PMEGridSizeZ 90

#99 on protein

#constraints off

#consref LacYO-POPE-restraint-2.pdb

#conskfile LacYO-POPE-restraint-2.pdb

#conskcol B

#heave bgal fixe

#fixedatoms on

#fixedatomsfile LacY+H-o-pose-1.ref

#fixedatomscol B

#fixedatomsforces on

langevin on

langevinDamping 5

langevinTemp 310

useGroupPressure yes #must be used with rigigBonds (shake)

useFlexibleCell yes #box dimension can fluctuate

LangevinPiston on #use Langevin piston pressure control

LangevinPistonTarget 1.0 #pressure in bar

LangevinPistonPeriod 200

LangevinPistonDecay 100

LangevinPistonTemp 310

TMD on

TMDk 7 #Elestic constant (kcal/mol/Å)

TMDOutputFreq 1000

TMDFile Lac-occl+H+TMD.pdb

TMDFirstStep 0

TMDLastStep 10000000

#TMDInitialRMSD 0

TMDFinalRMSD 0

#TMDDiffRMSD off

#TMDFile2

############################################################
#####################

Lutimba Stuart
Masters Student
Skovde University Sweden
Science for Life Laboratory (Scilife) Sweden

This archive was generated by hypermail 2.1.6 : Tue Sep 17 2019 - 23:19:40 CDT