RE: TMD simulations

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Mon May 03 2010 - 21:25:29 CDT


Hi Yang

 

That is just what I want to know. Thanks a lot. So I have one more question, rmsd is calculated from all atoms of target structure or only from backbone ones??

 

King reguards

 

Andres







Date: Mon, 3 May 2010 08:57:07 -0500
Subject: Re: namd-l: TMD simulations
From: yanggao_at_iastate.edu
To: andresmoralesn2_at_hotmail.com


hi, Andres
the 3rd column means the expected rmsd value for your simulation. As you defined the starting and target structures, the initial rmsd (Ir) is fixed, and you also define TMDFInalRMSD (Fr), here is 0. So the program expect the rmsd decreases linearly upon time, the 3rd column = Ir - (Ir - Fr)*timestep/overalltime; the 4th column is the actual rmsd of your current structure and target structure. The force acts on the simulation system is proportional to the square of (3rd column-4th column). Hope it answer your question.

Yang


2010/4/30 Andres Morales N <andresmoralesn2_at_hotmail.com>


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 0.0000 0.0000 13820.6814 &nbs! p; -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
bi! ncoordinates 1hgf_equil.coor
binvelocities 1hgf_equil.vel � �実匸黼�阨��釶辣�塒吊鈿迚郤岱丈蜥齡�辣齡辮�絢岱嬢�齡辮�碓旭旭実匸�������������������������������岱升�喇葉盟塢藁�仭卅妖堙厶��実匸�������������������������������岱升�侮頤�岱情癇疽岦綯葹鴉�闔実匸鞜鱇辣�鴦�鞜鰡瘡豌貨頏阡�鉋�実匸 
# 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
 
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Boundary conditions
#wrapWater on
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamp! ing 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 300
langevinHydrogen off ;# don't couple langevin bath to hydrogens
 
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Targeted
TMD on
TMDk 200
TMDFirstStep 0
TMDLastStep 100000
TMDfile 1htm_equil.pdb
TMDFinalRMSD 0




Explore the seven wonders of the world Learn more!

                                               
_________________________________________________________________
News, entertainment and everything you care about at Live.com. Get it now!
http://www.live.com/getstarted.aspx

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:57 CST