hi
i m doing simulation membrane protein
while scaling down the lipids by a factor of 0.95 then performing EM
Steepest Descents converged to Fmax 10 in 18 steps
Potential Energy = -nan
Maximum force = 4.7791553e+02 on atom 5440
Norm of force = -nan
; minim.mdp - used as input
shikha agarwal wrote:
hi
i m doing simulation membrane protein
while scaling down the lipids by a factor of 0.95 then performing EM
Steepest Descents converged to Fmax 10 in 18 steps
Potential Energy = -nan
Maximum force = 4.7791553e+02 on atom 5440
Norm of force = -nan
;
hi
I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk .
when i skiped scaling by factor 0.95 then , after EM step I m getting same
potential energy nan result.
i m doing simulation membrane protein
while scaling down the lipids by a factor of 0.95 then performing EM
Steepest
shikha agarwal wrote:
hi
I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk .
What is the hardware type? PowerPC, Intel 32- or 64-bit, etc?
when i skiped scaling by factor 0.95 then , after EM step I m getting
same potential energy nan result.
Do other simple systems work?
hi
I m using gromacs4.5.3 . hardware 1GB ram 320 hard disk .
Intel 32. I can perform simple task .
I m trying nstxout=1 in my .mdp file. I will report u later.
What is the hardware type? PowerPC, Intel 32- or 64-bit, etc?
when i skiped scaling by factor 0.95 then , after EM step I m
hi,
I m tried nstxout=1 in my .mdp file.
Potential Energy = -nan
Maximum force = 3.5637456e+07 on atom 2455
Norm of force = -nan
help me!
regards:
shikha
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
shikha agarwal wrote:
hi,
I m tried nstxout=1 in my .mdp file.
Potential Energy = -nan
Maximum force = 3.5637456e+07 on atom 2455
Norm of force = -nan
help me!
The purpose of nstxout=1 is not to give you a different result. It might aid
you in watching
hi,
I tried on other system , 4GB ram , core i3 ,64bit processor
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 10.0
shikha agarwal wrote:
hi,
I tried on other system , 4GB ram , core i3 ,64bit processor
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
Hi users,
I am running a very simple simulation of methane inside a pore (v.much
like a carbon nanotube but in my case the tube is supposed to
represent silica.) I keep this tube frozen.
I start with an energy minimisation-however this runs to completion
almost instantly and I keep get
Jennifer Williams wrote:
Hi users,
I am running a very simple simulation of methane inside a pore (v.much
like a carbon nanotube but in my case the tube is supposed to represent
silica.) I keep this tube frozen.
I start with an energy minimisation-however this runs to completion
almost
Manik Mayur wrote:
2009/9/8 Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
Jennifer Williams wrote:
Hi users,
I am running a very simple simulation of methane inside a pore
(v.much like a carbon nanotube but in my case the tube is
2009/9/8 Mark Abraham mark.abra...@anu.edu.au
Jennifer Williams wrote:
Hi users,
I am running a very simple simulation of methane inside a pore (v.much
like a carbon nanotube but in my case the tube is supposed to represent
silica.) I keep this tube frozen.
I start with an energy
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?
Am Mittwoch, 20. Juni 2007 schrieb Sheyore Omovie:
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
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
.
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
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
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
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