From: Christopher Hartshorn (cmhartshorn_at_gmail.com)
Date: Thu Mar 12 2009 - 00:35:02 CDT
Chris,
Attached below this is my conifg file. Yes it is possible that I do
not have a full understanding of the process. My idea about the
script from the tutorial (that I am using) is that it runs the sim/FEP
for lambda step X for n iterations and then repeats for the next
lambda step and so on. The restart file is created for each 1000 fs
and there are 85000 in mine per lambda step. So, if I have a restart
at 55000 of a particular lambda step then when I restart I will be in
the middle of the n iterations. My understanding about this is that
the purpose of the numerous iterations at each step is to allow
convergence upon some dG value or more simply to allow for sufficient
sampling. Thus, if I restart at some point (such as 55K of an 85K)
will it still be at the same energy as before it crashed or does it
require another 85K n steps to converge to a "reportable" value for
the lambda step it had been trying to calculate? Or am just not
getting how this is actually run in NAMD?
Best,
Chris
#############################################################
## JOB DESCRIPTION ##
#############################################################
# FEP
# DMPC and prot mid1 -upper half vanishing
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure dmpc_mid1.psf
coordinates mdsim2ns_out.coor
velocities mdsim2ns_out.vel
extendedSystem mdsim2ns_out.xsc
set outputname dmpcmid1FEP55ksteps04_out
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input parameters
paraTypeCharmm on
parameters par_all27_prot_lipid_sil.inp
parameters par-extraterms.inp
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 1.0 ;# 1fs/step
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
# An internal tuning parameter used in determining the size of the
cubes of
# space with which NAMD uses to partition the system
# The z dimension is going to shrink so pad sufficiently
margin 1
wrapWater on
wrapNearest off
# PME (for full-system periodic electrostatics) only with PBC's
# Must get cell dimensions from PBC basisvectors for accurate PME
# Remember multiples of 2,3, and/or 5
PME on
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 100
# Constant Pressure Control (variable volume) only for PBC's
useGroupPressure yes # smaller fluctuations
useFlexibleCell no # allow dimensions to fluctuate independently
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 10 ;# damping coefficient (gamma) of 10/ps
langevinTemp 310
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Nos´e-Hoover Langevin piston pressure control
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.0
langevinPistonDecay 100.0
langevinPistonTemp 310
# Output
outputName $outputname
restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 100
outputTiming 100
outputPressure 100
binaryoutput off
rigidbonds all
rigidtolerance 0.000001
rigiditerations 400
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fix.pdb
fixedAtomsCol B
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# FEP
source fep.tcl
fep on
fepFile dmpc_mid1_FEP.fep
fepCol B
fepOutFile DMPCmid155ksteps04.fepout
fepOutFreq 10
# LOOP OVER LAMBDA-STATES
fepEquilSteps 5000
set nSteps 85000
set dLambda 0.04
set init {0.0 0.00001 0.0001 0.001 0.01 0.02}
set end {0.98 0.99 0.999 0.9999 0.99999 1.0}
runFEPlist $init $nSteps
runFEP 0.02 0.98 $dLambda $nSteps
runFEPlist $end $nSteps
On Mar 11, 2009, at 5:53 PM, Chris Harrison wrote:
> Chris,
>
> I can't think of a reason an FEP could not be restarted. I think you
> maybe confusing the way FEP works inside NAMD with the way one of the
> example tcl scripts works that allows you to do a full series of
> lambda values in a single NAMD config script. Can you send your
> namd config file?
>
> C.
>
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
> Christopher Hartshorn <cmhartshorn_at_wsu.edu> writes:
>> Date: Wed, 11 Mar 2009 17:34:59 -0700
>> From: Christopher Hartshorn <cmhartshorn_at_wsu.edu>
>> To: namd-l_at_ks.uiuc.edu
>> Subject: namd-l: FEP restart?
>> Return-Path: char_at_halifax.ks.uiuc.edu
>> Message-Id: <D90DD937-EB7C-4F36-9AC3-1B02777FE188_at_wsu.edu>
>> X-Spam-Status: No, score=-2.3 required=5.0 tests=AWL,BAYES_00
>> autolearn=unavailable version=3.1.7-0+tcb1
>>
>> Hello all. Recently, my dept. lost power during a snow storm here in
>> Pullman. Unfortunately, I did not have a few of the computers on a
>> power backup system and two sims were stopped before they had
>> ripened,
>> if you will.
>>
>> One of the sims was an FEP calculation, which brings me to my
>> question
>> of can an FEP be restarted? I had the restart feature on, of course,
>> for the usual every 1000 steps, but the more I think about it the
>> more I
>> wondered whether this matters. If my last restart file was from the
>> 55000 n step of lambda step .50 to .54 (there are 80K total n steps/
>> lambda step) then my restart would be in the middle of the n
>> iterations
>> and I could not start from this point (as far as I understand, at
>> least).
>> I can only restart, I think, from the beginning of the lambda step
>> (as
>> in at the n=0 point). Thus, am I correct in my thinking about
>> this, that
>> I need to rerun the entire FEP because I do not have a restart
>> point at
>> the beginning of some lambda step? And, on that same note for the
>> future, should I set my restart step number to the same as my n
>> iterations number (e.g. restart=80K steps if n steps=80K) so that
>> each
>> restart file set will be only at the beginning of the lambda step?
>> Thank you very much for any and all answers.
>>
>> Best,
>>
>> Chris
>> WSU
>>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:28 CST