[gmx-users] potential energy =nan
Sheyore Omovie
omovie_johnnie at hotmail.com
Wed Jun 20 19:17:51 CEST 2007
Hi,
I figured it might be neccessary to show my *.top file and coordinate file
(b4 solvation) so I could easily get help.
Rgds
John
; File 'twopoly.top' was generated
; By user: sjomovie (1028)
; On host: bmp041.biophysics.net
; At date: Tue Jun 19 23:12:16 2007
;
; This is your topology file
; Great Red Oystrich Makes All Chemists Sane
;
; Include forcefield parameters
#include "ffG43a1.itp"
; Include chain topologies
#include "twopoly_B.itp"
#include "twopoly_A.itp"
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Great Red Oystrich Makes All Chemists Sane in water
[ molecules ]
; Compound #mols
Protein_B 1
Protein_A 1
SOL 314583
TITLE Great Red Oystrich Makes All Chemists Sane
REMARK THIS IS A SIMULATION BOX
CRYST1 10.266 5.723 2.981 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 N ALA B 1 -0.677 -1.23 -0.491 1 0
ATOM 2 H1 ALA B 1 -1.667 -1.089 -0.491 1 0
ATOM 3 H2 ALA B 1 -0.414 -1.744 -1.307 1 0
ATOM 4 H3 ALA B 1 -0.414 -1.744 0.325 1 0
ATOM 5 CA ALA B 1 -0.001 0.064 -0.491 1 0
ATOM 6 CB ALA B 1 -0.509 0.856 0.727 1 0
ATOM 7 C ALA B 1 1.499 -0.11 -0.491 1 0
ATOM 8 O ALA B 1 2.065 -0.922 0.251 1 0
ATOM 9 N GLY B 2 2.311 0.711 -1.4 1 0
ATOM 10 H GLY B 2 1.979 1.399 -2.045 1 0
ATOM 11 CA GLY B 2 3.7 0.321 -1.173 1 0
ATOM 12 C GLY B 2 4.606 1.528 -1.169 1 0
ATOM 13 O GLY B 2 4.515 2.418 -2.019 1 0
ATOM 14 N ALA B 3 5.629 1.648 -0.12 1 0
ATOM 15 H ALA B 3 5.805 1.002 0.622 1 0
ATOM 16 CA ALA B 3 6.336 2.899 -0.378 1 0
ATOM 17 CB ALA B 3 5.719 3.979 0.528 1 0
ATOM 18 C ALA B 3 7.821 2.735 -0.164 1 0
ATOM 19 O1 ALA B 3 8.258 1.505 0.219 1 0
ATOM 20 O2 ALA B 3 8.599 3.831 -0.372 1 0
ATOM 21 N ALA A 4 -0.677 -1.23 -0.491 1 0
ATOM 22 H1 ALA A 4 -1.667 -1.089 -0.491 1 0
ATOM 23 H2 ALA A 4 -0.414 -1.744 -1.307 1 0
ATOM 24 H3 ALA A 4 -0.414 -1.744 0.325 1 0
ATOM 25 CA ALA A 4 -0.001 0.064 -0.491 1 0
ATOM 26 CB ALA A 4 -0.509 0.856 0.727 1 0
ATOM 27 C ALA A 4 1.499 -0.11 -0.491 1 0
ATOM 28 O ALA A 4 2.065 -0.922 0.251 1 0
ATOM 29 N ALA A 5 2.311 0.711 -1.4 1 0
ATOM 30 H ALA A 5 1.979 1.399 -2.045 1 0
ATOM 31 CA ALA A 5 3.7 0.321 -1.173 1 0
ATOM 32 CB ALA A 5 4.079 -0.705 -2.254 1 0
ATOM 33 C ALA A 5 4.606 1.529 -1.169 1 0
ATOM 34 O ALA A 5 4.515 2.421 -2.021 1 0
ATOM 35 N ALA A 6 5.629 1.648 -0.119 1 0
ATOM 36 H ALA A 6 5.806 1.001 0.623 1 0
ATOM 37 CA ALA A 6 6.335 2.9 -0.377 1 0
ATOM 38 CB ALA A 6 5.718 3.979 0.529 1 0
ATOM 39 C ALA A 6 7.821 2.736 -0.163 1 0
ATOM 40 O1 ALA A 6 8.258 1.506 0.219 1 0
ATOM 41 O2 ALA A 6 8.599 3.832 -0.37 1 0
TER
ENDMDL
>From: "Sheyore Omovie" <omovie_johnnie at hotmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] potential energy =nan
>Date: Wed, 20 Jun 2007 11:44:32 -0500
>
>Hi Mark,
>I'm sorry, I assume you'll understand that I've carried out all the steps
>before an EM run.
>David said is because the coordinates are on top of each other, I'll
>appreciate any more specific advice on how to fix this.
>Meanwhile, I'll try Martin's advice on making the water flexible.
>Rgds
>John
>
>
>>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>Subject: Re: [gmx-users] potential energy =nan
>>Date: Wed, 20 Jun 2007 23:09:03 +1000
>>
>>Sheyore Omovie wrote:
>>>I am doing an Energy Minimisation run for two polypeptides in a box. I
>>>get the range checking error, variable ci= .... and the simulation
>>>crashes. After changing ns_type to simple, the simulation is running, but
>>>very slowly and the first few steps return Epot=nan.
>>>What could I have done wrong?
>>
>>It's hard to tell from your description, since an energy minimization is
>>not a simulation... but please try following this general scheme
>>http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
>>
>>Mark
>>_______________________________________________
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