Re: Energy minimization

From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Tue Jun 28 2011 - 18:49:01 CDT

Hi,

I have done the minimzation of the protein ligand complex using this
configuration :-

numsteps 10000
minimization on
dielectric 1.0
coordinates ../common/complex_ionized.pdb
outputname complex_eq
outputEnergies 1000
binaryoutput no
DCDFreq 1000
restartFreq 1000
structure ../common/complex_ionized.psf
paraTypeCharmm on
parameters ../common/par_all27_prot_na.prm
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 10

Here is the result of the o/p file :-

TIMING: 10000 CPU: 1722.01, 0.172174/step Wall: 1722.01, 0.172174/step, 0
hours remaining, 41.582031 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED IMPRP
              ELECT VDW BOUNDARY MISC
 KINETIC TOTAL TEMP POTENTIAL TOTAL3
     TEMPAVG

ENERGY: 10000 1840.8235 1745.8578 816.0522 29.3870
        -60461.3391 6405.1479 0.0000 0.0000
0.0000 -49624.0707 0.0000 -49624.0707 -49624.0707
    0.0000

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
WRITING COORDINATES TO DCD FILE AT STEP 10000
WRITING COORDINATES TO RESTART FILE AT STEP 10000
FINISHED WRITING RESTART COORDINATES
The last position output (seq=10000) takes 0.002 seconds, 41.582 MB of
memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 10000
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=10000) takes 0.001 seconds, 41.582 MB of
memory in use
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10000
WRITING COORDINATES TO OUTPUT FILE AT STEP 10000
CLOSING COORDINATE DCD FILE
The last position output (seq=-2) takes 0.064 seconds, 41.582 MB of memory
in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP 10000
The last velocity output (seq=-2) takes 0.043 seconds, 41.582 MB of memory
in use

I am trying to plot the TOTAL v/s TS to look for the stability of system
after minimization using VMD-> extension->analysis->NAMD plot . But I am not
getting any plot between TOTAL and TS ???... Also I want to know how to look
to for the stability of the system after minimization apart from plotting
values or plot itself is enough ??

Pls help

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010_at_yahoo.com

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