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" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@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 <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@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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