Taking a shot in the dark, when it happens immediately like that (step0) in
my experience it often means the topology is wrong.
On 10 Oct 2013 16:27, "Justin Lemkul" wrote:
>
>
> On 10/10/13 10:21 AM, Nikhil Agrawal wrote:
>
>> DearAll,
>>
>> when I am running NVT equilibration phase i am getting
On 10/10/13 10:21 AM, Nikhil Agrawal wrote:
DearAll,
when I am running NVT equilibration phase i am getting following error
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4#
Wrote pdb files with previous and current coordinates
starting mdrun 'Gromacs Runs On Most of All Computer Syst
DearAll,
when I am running NVT equilibration phase i am getting following error
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4#
Wrote pdb files with previous and current coordinates
starting mdrun 'Gromacs Runs On Most of All Computer Systems in water'
25 steps,500.0 ps.
WARNIN
decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
Would you please give me your suggestions?
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To: Justin Lemkul ; "gmx-users@gromacs.org"
Cc:
Se
r suggestions.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Wednesday, May 8, 2013 5:07 PM
Subject: Re: [gmx-users] unstable system
On 5/8/13 2:35 AM, Shima Arasteh wrote:
> OK.
>
> 1. Exact command
l
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Wednesday, May 8, 2013 5:07 PM
Subject: Re: [gmx-users] unstable system
On 5/8/13 2:35 AM, Shima Arasteh wrote:
> OK.
>
> 1. Exact commands given in the preparation protocol (EM and equilibration)
>
> EM:
> #
On 5/8/13 2:35 AM, Shima Arasteh wrote:
OK.
1. Exact commands given in the preparation protocol (EM and equilibration)
EM:
# grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr
#mdrun -deffnm minim
NVT:
#grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
#mdrun -deffnm n
: Discussion list for GROMACS users
Cc:
Sent: Wednesday, May 8, 2013 2:16 AM
Subject: Re: [gmx-users] unstable system
On 5/7/13 2:42 PM, Shima Arasteh wrote:
> Hi,
>
> I have run a new npt after energy minimization on my system composed of
> water/protein/lipid/ions.
> After a few nanosec
Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, April 19, 2013 11:29 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 2:57 PM, Shima Arasteh wrote:
> Thanks so much for your replies. I appreciate you.
> Do you think that more NPT equilibration might solve the probl
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, April 19, 2013 11:29 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 2:57 PM, Shima Arasteh wrote:
> Thanks so much for your replies. I appreciate you.
> Do you
On 4/19/13 2:57 PM, Shima Arasteh wrote:
Thanks so much for your replies. I appreciate you.
Do you think that more NPT equilibration might solve the problem? or wont work?
I have no idea at what point you are in your procedure that is crashing. I'm
not going to make some blind assessment
: [gmx-users] unstable system
On 4/19/13 2:49 PM, Shima Arasteh wrote:
> The energy minimization has been done and the result is as follow:
>
> Steepest Descents converged to Fmax < 100 in 8971 steps
> Potential Energy = -1.5253394e+06
> Maximum force = 9.2729095e+01 on a
On 4/19/13 2:49 PM, Shima Arasteh wrote:
The energy minimization has been done and the result is as follow:
Steepest Descents converged to Fmax < 100 in 8971 steps
Potential Energy = -1.5253394e+06
Maximum force = 9.2729095e+01 on atom 4719
Norm of force = 3.5977371e+00
But by runn
teh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, April 19, 2013 10:02 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 1:18 PM, Shima Arasteh wrote:
> Lets check the minim.mdp settings:
>
> ( ff applied is charmm36)
> define = -DPOSRES
> integrator
On 4/19/13 1:18 PM, Shima Arasteh wrote:
Lets check the minim.mdp settings:
( ff applied is charmm36)
define = -DPOSRES
integrator= steep
emtol= 100.0
emstep= 0.01
nsteps= 5
nstlist= 1
ns_type= grid
rlist= 1.2
rlistlong
users
Cc:
Sent: Friday, April 19, 2013 8:42 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:55 AM, Shima Arasteh wrote:
> All right.
> And if minimization doesnt fix such a problem, what would be the solution?
> However I have not tried it on my own system yet.
>
>
:-)
OK, thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, April 19, 2013 8:42 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:55 AM, Shima Arasteh wrote:
> All right.
> And if minimization
: Shima Arasteh ; Discussion list for GROMACS users
Cc:
Sent: Friday, April 19, 2013 8:22 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:43 AM, Shima Arasteh wrote:
Thanks for your reply.
I' d like to know if I need to remove all position restraints before
MDRUN?means that
8:22 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:43 AM, Shima Arasteh wrote:
> Thanks for your reply.
>
> I' d like to know if I need to remove all position restraints before
> MDRUN?means that the last step of npt should be done without position
> restraint
58 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:26 AM, Shima Arasteh wrote:
Hi,
I tried to equilibrate my system by setting timestep=1 fts and decreasing the
position restraints step by step.
But when I go to MDRUN step, it doesnt work and some pdb files are printed.
what is print
Sent: Friday, April 19, 2013 7:58 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:26 AM, Shima Arasteh wrote:
> Hi,
>
> I tried to equilibrate my system by setting timestep=1 fts and decreasing the
> position restraints step by step.
>
> But when I go to MDRUN step,
: Shima Arasteh ; Discussion list for GROMACS users
Sent: Sunday, April 7, 2013 4:46 PM
Subject: Re: [gmx-users] unstable system
On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh
wrote:
Hi all,
I have a system of peptide/POPC/water/ions. The energy minimization and NVT
steps has passed
: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Sunday, April 7, 2013 4:46 PM
Subject: Re: [gmx-users] unstable system
On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh
wrote:
Hi all,
>
> I have a system of peptide/POPC/water/ions. The energy minimization a
tep to 1 fs for a period of time.
-Justin
> Many thanks for your replies.
>
>
> Sincerely,
> Shima
>
>
>
> From: Justin Lemkul
> To: Shima Arasteh ; Discussion list for
> GROMACS users
> Sent: Sunday, April 7, 2013 4:46 PM
&g
thanks for your replies.
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Sunday, April 7, 2013 4:46 PM
Subject: Re: [gmx-users] unstable system
On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh
wrote
On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh
wrote:
> Hi all,
>
> I have a system of peptide/POPC/water/ions. The energy minimization and
> NVT steps has passed successfully. I ran NPT step for around 10 ns with
> restraints of protein and P atoms at first nano seconds and then removing
> them g
Hi all,
I have a system of peptide/POPC/water/ions. The energy minimization and NVT
steps has passed successfully. I ran NPT step for around 10 ns with restraints
of protein and P atoms at first nano seconds and then removing them gradually.
I tried to go on MDRUN. I did not remove restraint o
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