Re: constant temprature for vacuum condition in namd file

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 19 2018 - 14:26:48 CDT

Hi Soroush, considering this and the previous messages posted by you, a
friendly advice is the following: please sit down, breathe deeply, and
start reading about the fundamentals of MD and the technical documentation
of the basic features of NAMD or similar codes.

You mentioned earlier that "you are in a hurry", which obviously affects
your decisions.

You should keep in mind that NAMD (and other scientific codes) will only
raise an error for those conditions that make it impossible for them to
run. *In many cases, they will not raise errors if the input of the
simulation is technically functional but represents a completely unphysical
condition, which would be just as useless to you.*

Invest some time now: it will save you a lot of time later.

Giacomo

On Fri, Oct 19, 2018 at 3:21 PM soroush ziaei <soroush.ziaei7337_at_gmail.com>
wrote:

> hi.
> i dealt with an error in terminal about constant temperature for fep
> simulation in vaccum, that says; Alchemical FEP can be performed only in
> constant temperature simulations.
> i puted the last config file (equilibrium) below:
>
> #2.namd
> numsteps 15000
> structure fu.psf
> coordinates fu.pdb
> outputName eq2
> XSTfile eq2.xst
>
> bincoordinates eq1.coor
> binvelocities eq1.vel
> extendedSystem eq1.xsc
>
> langevin off
> langevinDamping 3
> langevinTemp 310
> langevinHydrogen on
>
>
> switching on
> switchDist 10
> cutoff 12
> pairlistdist 14
> margin 3
>
> binaryOutput yes
> binaryRestart yes
>
> parameters par file.par
> parameters par2.prm
> paraTypeCharmm on
> wrapAll yes
> wrapNearest yes
> COMmotion no
>
> outputEnergies 500
> outputTiming 500
> xstFreq 500
> dcdFreq 250
> restartFreq 500
>
> timestep 1
> nonBondedFreq 2
> fullElectFrequency 4
> stepsPerCycle 20
>
> Pme off
> PmeGridSizeX 40
> PmeGridSizeY 40
> PmeGridSizeZ 40
>
> exclude scaled1-4
> 1-4scaling 1
>
>
> alch on
> alchType FEP
> alchFile fu.fep
> alchCol B
> alchOutFile forward-off.fepout
> alchOutFreq 5
> set numSteps 500
>
> alchDecouple off
>
> set Lambda0 0.0
> set dLambda 0.1
>
> while {$Lambda0 <= 1.0} {
> alchLambda $Lambda0
> set Lambda0 [expr \$Lambda0 + \$dLambda]
> alchLambda2 $Lambda0
> run 10000
> }
>
>
> what's wrong with this part of config file to perform vacuum condition?
>
> regards, soroush
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

This archive was generated by hypermail 2.1.6 : Tue Nov 12 2019 - 23:20:04 CST