From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue May 10 2016 - 13:57:03 CDT
Sounds like it might be an issue with the box dimensions. Could you do a
measure minmax on your system to find out the max and min length on each
dimension? The difference between these would tell you the length of your
box in that dimension. Setting up box lengths by this method usually works
Hope this helps,
On Tue, May 10, 2016 at 9:41 AM, Srijita Paul <srijitap91_at_gmail.com> wrote:
> 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>
>>> 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 10000
>>>> 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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