From: Srijita Paul (srijitap91_at_gmail.com)
Date: Tue May 10 2016 - 08:41:10 CDT
my system contains a protein of 15 residue,choline-o-sulfate,urea and tip3p
water.i have prepared the system using packmol and psf is generated using
psfgen.there is total 50712 atoms in the pdb.according to Mr. Jeff i have
taken a large cubic box of length 120A.now minimisation and heating is
runing well in nvt.but after that when i am trying to equilibriate the
system in npt the following error is comming-FATAL ERROR: Incorrect atom
count in binary file protein_choline_urea_wat_nvt.restart.coor
the configuration files are attached below.
On Mon, May 9, 2016 at 9:37 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
> Hi Srijita,
> Could you provide some details on how you prepared the system? And what
> you have (i.e. protein, lipid, water, ions etc) in your system?
> On Mon, May 9, 2016 at 10:38 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>> I want to second Jeff’s comment: not-a-numbers in pressure and crazy
>> energies mean that your system is not constructed well. If you provide us
>> the full NAMD configuration file you use and the result of "measure minmax
>> [atomselect top all]" we will be able to see if there are any obvious
>> errors. You’ll have to find problems with the system, if any, yourself.
>> On May 8, 2016, at 20:19, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>> If you don't get reasonable energies after 10000 steps of minimization,
>> there is something wrong with how your system is constructed. Possible
>> problems can be a poorly chosen initial size or major clashes in the
>> initial structure.
>> Jeffrey Comer, PhD
>> Assistant Professor
>> Institute of Computational Comparative Medicine
>> Nanotechnology Innovation Center of Kansas State
>> Kansas State University
>> Office: P-213 Mosier Hall
>> Phone: 785-532-6311
>> Website: http://jeffcomer.us
>> On Sat, May 7, 2016 at 6:17 AM, Srijita Paul <srijitap91_at_gmail.com>
>>> I am facing a problem during minimisation and heating.The job is
>>> automatically being stopped after few steps showing such type of error-
>>> LINE MINIMIZER BRACKET: DX 0 inf DU -nan -nan DUDX nan nan nan
>>> MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
>>> LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
>>> Warning: Low global exclusion count! (92292 vs 92346)
>>> Warning: This warning is not unusual during minimization.
>>> Warning: Increasing pairlistdist or cutoff may avoid this.
>>> PRESSURE: 10000 -nan nan nan nan -nan nan nan nan -nan
>>> GPRESSURE: 10000 nan nan nan nan nan nan nan nan nan
>>> TIMING: 10000 CPU: 32969.1, 3.29687/step Wall: 32959, 3.29586/step, 0
>>> hours remaining, 1132.691406 MB of memory in use.
>>> ETITLE: TS BOND ANGLE DIHED
>>> IMPRP ELECT VDW BOUNDARY
>>> MISC KINETIC TOTAL TEMP
>>> POTENTIAL TOTAL3 TEMPAVG PRESSURE
>>> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>>> ENERGY: 10000 9999999999.9999 9999999999.9999 9999999999.9999
>>> 9999999999.9999 9999999999.9999 9999999999.9999 0.0000
>>> 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999
>>> 9999999999.9999 0.0000 9999999999.9999 9999999999.9999
>>> 1061208.0000 9999999999.9999 9999999999.9999
>>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 10000
>>> WRITING COORDINATES TO DCD FILE protein_choline_urea_wat_nvt.dcd AT STEP
>>> WRITING COORDINATES TO RESTART FILE AT STEP 10000
>>> FINISHED WRITING RESTART COORDINATES
>>> The last position output (seq=10000) takes 0.002 seconds, 1132.691 MB of
>>> memory in use
>>> WRITING VELOCITIES TO RESTART FILE AT STEP 10000
>>> FINISHED WRITING RESTART VELOCITIES
>>> REINITIALIZING VELOCITIES AT STEP 10000 TO 310 KELVIN.
>>> TCL: Running for 10000 steps
>>> FATAL ERROR: Low global exclusion count! (92292 vs 92346) System
>>> unstable or pairlistdist or cutoff too small.
>>> In my configuration file cutoff is 12 and pairlistdist is 14.
>>> My system contains protein urea choline-o-sulfate and water.total there
>>> is 50712 atoms.Box volume 100*100*100.
>>> please give me some guidance about it.
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