Re: FW: TMD simulations

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Fri Apr 30 2010 - 21:21:15 CDT

Hi Andres,

You will find the answer to your question in the most likely of locations:
http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node41.html

Josh

On Apr 30, 2010, at 8:42 PM, Andres Morales N wrote:

>
>
>
> Dear NAMD users
>
>
> I carried out TMD simulations of a polypeptide of hemaglutinin. I was analysing log file but I do not know what the third and fourth columns means. I think the last one has information about rmsd respect target structure, but i am not sure. I wait somebody can help me with it. Thanks
>
> Andres
>
> ENERGY: 0 123.9492 325.1711 158.8218 15.9574 -87899.1085 8291.3290 &n! bsp; 0.0000 0.0000 13820.6814 -65163.1986 298.3264 -65155.0510 -65155.0510 298.3264
> TMD 1 14.773 14.7732
> TMD 2 14.7728 14.7732
> TMD 3 14.7727 14.7733
> TMD 4 14.7725 14.7733
> TMD 5 14.7724 14.7733
> TMD 6 14.7722 14.7732
> TMD 7 14.7721 14.773
> TMD 8 14.7719 14.7727
> TMD 9 14.7718 14.7724
> TMD 10 14.7716 14.7719
>
>
> I used the following script to run the simulation:
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> ############################################################! #
> ## ADJUSTABLE PARAMETERS ##
> ##########################! ######## ###########################
> structure 1hgf.psf
> coordinates 1hgf.pdb
> bincoordinates 1hgf_equil.coor
> binvelocities 1hgf_equil.vel
> $B!!(B
> set outputname TMD_nomin
> firsttimestep 0
> numsteps 100000
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> # Input
> paraTypeCharmm on
> parameters par_all22_prot.inp
> $B!!(B
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 8.
> pairlistdist 13.5
> margin 0
> # Integrator Parameters
> timestep 1.0 ;# 1fs/step
> rigidBonds all ;# needed for 1fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
> # Output
> outputName $outputname
> dcdfreq 1000
> outputEnergies 10
> $B!!(B
> #############################################################
> ## EXTRA PARAMETERS ##
> ###########################################! ##################
> # Boundary conditions
> #wrapWater on
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp 300
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
> $B!!(B
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
> # Targeted
> TMD on
> TMDk 200
> TMDFirstStep 0
> TMDLastStep 100000
> TMDfile 1htm_equil.pdb
> TMDFinalRMSD 0

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