From: lily jin (lily1907_at_yahoo.com)
Date: Fri Nov 02 2007 - 10:43:55 CDT
Dear all,
I am trying to run TMD in NAMD. The first time I let it run 10000time steps, but it couldn't reach the target conformation rff1. The second time I let it run 15000 time steps, it past the target conformation, but never matchs the target conformation. TMD ends at:
case 1(10000 steps):
TMD 9998 0.00134302 3.73678
TMD 9999 0.000671509 3.73699
case2(15000 steps):
TMD 14998 0.000895345 3.65115
TMD 14999 0.000447672 3.65091
Below is my scripts. Can you give me some advice? Thank you very much!
-------------------------
# TMD from (rff0) to (rff1) structures
# parameters and files
structure ../work/frame0F01_autopsf.psf
coordinates ../work/rff0.pdb
outputName ../result/tmdrff0-rff1_protein_5000
set temperature 300
firsttimestep 0
numsteps 15000
#input
paraTypeCharmm on
parameters ../work/par_all27_prot_na.inp
temperature $temperature
#Force filed parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 14.
#restrains
#constraints on
#TDM parameters
TMD on
TMDk 200
TMDoutputFreq 1
TMDFile ../work/rff1.pdb
TMDFirststep 0
TMDLaststep 15000
#TMDInitialRMSD
TMDFinalRMSD 0
#Integrator Parameters
timestep 1.0
rigidBonds none
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 10
restartfreq 200
dcdfreq 100
xstFreq 200
outputEnergies 100
Lily
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