On 11/5/13 7:31 AM, Kalyanashis Jana wrote:
Dear Justin,
Can you please tell me, how I can solve this problem?? If I will change
the coordinate of atom 15461, will it help me? But you know, I did this
step changing the position of drug molecule and I got same error.
You should first do wh
Dear Justin,
Can you please tell me, how I can solve this problem?? If I will change
the coordinate of atom 15461, will it help me? But you know, I did this
step changing the position of drug molecule and I got same error.
On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul wrote:
>
>
> On 11/5/13
On 11/5/13 6:28 AM, Kalyanashis Jana wrote:
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces have
What does your curve look like? What parameters are you using in the mdp?
How big is your system and what kind of molecules are in there? Providing
this kind of information would help people work out what the problem is.
Then again it may be ok that the minimisation has converged without
reaching
On 11/3/13 6:20 AM, kiana moghaddam wrote:
Dear Justin
Further to your previous email, I want to calculate free energy for DNA-ligand
interaction. According to your answer, for more sensitive calculations like free
energy simulations and normal modes, emtolshould be lower than 1. As
I understa
On 11/2/13 3:38 PM, kiana moghaddam wrote:
Hi GMX Users
I 'm running MD Simulation for DNA-ligand interaction. I ran energy
minimization with emtol=10, 100 and 250 in 1 steps (steepest descent
followed by the conjugate gradient algorithm). The lowest value for energy
obtained for emtol=
On Sep 23, 2013 9:08 AM, "marzieh dehghan" wrote:
>
> Hi every body
> in order to protein- ligand docking, energy minimization was done by
> GROMACS. I did the following steps for insulin pdb file:
>
> 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
> 2- grompp -f em.mdp -c test.
On 9/23/13 3:08 AM, marzieh dehghan wrote:
Hi every body
in order to protein- ligand docking, energy minimization was done by
GROMACS. I did the following steps for insulin pdb file:
1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
2- grompp -f em.mdp -c test.pdb -p topol.top
On Tue, Mar 19, 2013 at 9:16 AM, Jeff Woodford <
jwoodf...@missouriwestern.edu> wrote:
> Greetings,
> I am relatively new to MD, and I am attempting to simulate a metal-organic
> framework but I don't seem to be even able to get past the energy
> minimization phase. I could appreciate any insight
Thank Justin so much !
On Sat, Feb 23, 2013 at 1:50 AM, Justin Lemkul wrote:
>
>
> On 2/21/13 9:10 PM, Kieu Thu Nguyen wrote:
>
>> Dear all,
>>
>> I can not distinguish when the Fmax < 10 kJmol-1nm-1, < 100, < 1000 ? is
>> appropriate
>>
>> Can anyone tell me which value is appropriate for li
On 2/21/13 9:10 PM, Kieu Thu Nguyen wrote:
Dear all,
I can not distinguish when the Fmax < 10 kJmol-1nm-1, < 100, < 1000 ? is
appropriate
Can anyone tell me which value is appropriate for lipid membrane, for
protein in water, for protein in lipid membrane ?
There is no absolute rule. Th
A couple of things:
1. Are your cutoffs appropriate for OPLS_AA? Even if you fix any code problems
and using the wrong cutoffs, your results will not be meaningful...
2. How are you generating your box/filling it with molecules? There are
indications that your original box is too small, or that
sion list for GROMACS users
> Sent: Sunday, December 16, 2012 11:18 AM
> Subject: Re: [gmx-users] Energy minimization
>
> Probably remove the overlapping lipid then. Once you run MD it will repack.
>
> On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote:
> > Thanks
d the overlapping atoms and
the reason of clashe among a vast number of atoms?
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: Shima Arasteh
Cc: Discussion list for GROMACS users
Sent: Sunday, December 16, 2012 11:18 AM
Subject: Re: [gmx-users] Energy minimization
Probably remov
It's printed in terminal, exactly before showing the values of infinite
potential and Max Force and .
Sincerely,
Shima
From: Dariush Mohammadyani
To: Shima Arasteh
Sent: Sunday, December 16, 2012 5:01 PM
Subject: Re: [gmx-users] Energy minimiz
Cc:
> Sent: Sunday, December 16, 2012 8:44 AM
> Subject: Re: [gmx-users] Energy minimization
>
> It depends on what the atom is overlapping with and some conjecture as to
> what might be causing the overlap:
>
> You can always manually move it, either by editing the .gro fil
-
From: Peter C. Lai
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Sunday, December 16, 2012 8:44 AM
Subject: Re: [gmx-users] Energy minimization
It depends on what the atom is overlapping with and some conjecture as to
what might be causing the overlap:
You can always manually
t; users
> Sent: Saturday, September 29, 2012 3:01 PM
> Subject: Re: [gmx-users] Energy minimization
>
>
>
> On 9/29/12 3:19 AM, Shima Arasteh wrote:
> >
> > Dear all,
> >
> > My system contains lipids, protein and water.
> > I want to energy mi
Subject: Re: [gmx-users] Energy minimization
On 9/29/12 3:19 AM, Shima Arasteh wrote:
>
> Dear all,
>
> My system contains lipids, protein and water.
> I want to energy minimize it, so ran grompp:
>
>
> # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
&g
On 9/29/12 3:19 AM, Shima Arasteh wrote:
Dear all,
My system contains lipids, protein and water.
I want to energy minimize it, so ran grompp:
# grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
and then:
# mdrun -v -deffnm em
The output is:
Steepest Descents:
Tolerance
It seems that your input structure has too severe clashes for energy
minimization, that there are problems with your topology, or that your mdp
options are not adequate. One possible solution, if your topology is correct,
is to first perform an energy minimization using soft-core potentials to g
Dear Erik,
I also encountered similar problem. So you mean it cannot be further energy
minimized? How can we proceed with NPT if the system is not in equilibrium?
On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund wrote:
>
> 26 sep 2012 kl. 08.16 skrev Shima Arasteh:
>
> > Dear all,
> >
> > My syst
26 sep 2012 kl. 08.16 skrev Shima Arasteh:
> Dear all,
>
> My system contains lipids, protein and water.
> I want to energy minimize it, so ran grompp:
>
>
> # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr
>
> and then:
> # mdrun -v -deffnm em
>
>
> The output is:
> Steepe
:12 Mittwoch, 19.September 2012
Betreff: Re: [gmx-users] Energy Minimization of Alanin
for EM you can probably ignore this, but note that these are the wrong
cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch).
On 2012-09-19 11:04:47AM +0100
for EM you can probably ignore this, but note that these are the wrong
cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch).
On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote:
> Hello
>
> I want to do md simulations with the amino acid alanin fo
On 9/19/12 6:04 AM, Lara Bunte wrote:
Hello
I want to do md simulations with the amino acid alanin for practice. I choose
alanin because it is parametrized in my forcefield. I use charmm27.
I created with pdb2gmx my topology and I use water model tip3p. I choosed a
dodecahedron box with dis
On 6/8/12 3:15 PM, Hicks, Erica wrote:
Hi,
I am working through the KALP-15 tutorial and having difficulties getting the
correct area per lipid (~71 A^2). I first scaled the lipid by a factor of 4
(perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) then
did energy minimiza
Hi Mark,
Thanks - I completely forgot about that!
Cheers,
Huiwen
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Mark Abraham
Sent: Sunday, March 18, 2012 2:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimization of
On 18/03/2012 1:01 PM, NG HUI WEN wrote:
Hi all,
I have a seemingly simple task that turned quite tricky here.
I am trying to perform energy minimization on a crystal structure
after adding hydrogen to the protein using pdb2gmx (OPLS).
The problem I am facing now is that after energy minimi
On 11/02/2012 4:15 AM, francesca vitalini wrote:
Ok now I have tryied to restart it all and the problem seems to be
that the system has some overlapping. In fact, no matter what I
freeze, water, CA or nothing, I get this error message
VERSION 3.3.1
This program is free software; you
On 11/02/2012 2:48 AM, francesca vitalini wrote:
In fact in the reverse transformation I'm feeding the CG structure
information.
Yes, but you need a source of atomistic intra-residue knowledge about
protein structure in order to convert a CG structure to something that
is vaguely plausible at
Ok now I have tryied to restart it all and the problem seems to be that the
system has some overlapping. In fact, no matter what I freeze, water, CA or
nothing, I get this error message
VERSION 3.3.1
This program is free software; you can redistribute it and/or
modify it under
In fact in the reverse transformation I'm feeding the CG structure
information.
Once I look through VMD to the FG structure I notice that the backbones are
not in planes so definitely I need to run some minimization there. In the
tutorial they were using simulating annealing, but I don't think I ne
On 11/02/2012 12:41 AM, francesca vitalini wrote:
In order to overcome the problem I tried to fix everything except the
backbone (solvent, sidechain and CA, as I want the structure to be
maintained). However, if I do then I have problems with the energy
minimization as the force on the 15300 is
In order to overcome the problem I tried to fix everything except the
backbone (solvent, sidechain and CA, as I want the structure to be
maintained). However, if I do then I have problems with the energy
minimization as the force on the 15300 is infinite.
Getting Loaded...
Reading file EM1-1.tpr,
francesca vitalini wrote:
I achieve
Steepest Descents converged to machine precision in 205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom 1520(parto of the
protein)
Norm of force = 2.2836
I achieve
Steepest Descents converged to machine precision in 205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom 1520(parto of the
protein)
Norm of force = 2.28369808518165e+06
and the system l
francesca vitalini wrote:
Tryed the double precision without any success... Again the same type of
error message. Might need to try other minimization algorithm. Any
suggestions on that?
What is the Fmax you achieve, and what are your intents for this process?
Minimizing very low is only
Tryed the double precision without any success... Again the same type of
error message. Might need to try other minimization algorithm. Any
suggestions on that?
2012/2/9 Justin A. Lemkul
>
>
> francesca vitalini wrote:
>
>> Hi all!
>> I'm trying to run some energy minimization with gromacs 3.3.1
francesca vitalini wrote:
Hi all!
I'm trying to run some energy minimization with gromacs 3.3.1 on a
system that I have transformed from cg to aa. After the reverse
transformation I solvate the system and I try to minimize just the
proteins (my system is a dimer) keeping fixed the water. The
On 10/01/2012 10:46 PM, Steven Neumann wrote:
Thank you. Imagine I would like to put ligands in further simulations.
Should I then copy coordinates of my ligands in smaller box (not to
overlap my tube) and then copy both coordinates of ions and ligands
plus protein?
Any way you want to constr
Thank you. Imagine I would like to put ligands in further simulations.
Should I then copy coordinates of my ligands in smaller box (not to overlap
my tube) and then copy both coordinates of ions and ligands plus protein?
On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham wrote:
> On 10/01/2012 10:13
On 10/01/2012 10:13 PM, Steven Neumann wrote:
Thank you. Should I also copy and paste coordinates of my ions or just
my protein?
The randomly-placed ions will be immaterial for EM.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Ple
Thank you. Should I also copy and paste coordinates of my ions or just my
protein?
Steven
On Tue, Jan 10, 2012 at 11:03 AM, Mark Abraham wrote:
> On 10/01/2012 9:54 PM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>> I am setting up my simulations of carbon tube with protein. I solvated my
>> syst
On 10/01/2012 9:54 PM, Steven Neumann wrote:
Dear Gmx Users,
I am setting up my simulations of carbon tube with protein. I solvated
my system, added ions and I would like to run EM of my system. My
carbons of the tube in MD will be restrained. In this case should I
run EM of my protein in wate
On 2011-05-21 09.09, sreelakshmi ramesh wrote:
Dear all,
I am using tabulated potential do simulate nacl in water
.when i was doing my energy minimization it gives me the following
error.Any help please..
Do you mean to say your table is correct?
Check the derivative numerically
Ok thanks
On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul wrote:
>
>
> Kavyashree M wrote:
>
>> Dear gromacs users,
>>
>> While doing energy minimization for a protein (from pdb), with oplsaa
>> force field
>> and tip4p water model, there was an error and em stopped -
>>
>> Fatal error:
>> A c
Kavyashree M wrote:
Dear gromacs users,
While doing energy minimization for a protein (from pdb), with oplsaa
force field
and tip4p water model, there was an error and em stopped -
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your
On 30/01/11 16:13, David van der Spoel wrote:
On 2011-01-30 17.08, ms wrote:
On 30/01/11 15:41, David van der Spoel wrote:
Since I have exactly the same needs (charged system in vacuum) I jump
in...
In http://www.gromacs.org/Documentation/Errors
it says:
Note for PME users: It is possible to
On 30/01/11 16:13, David van der Spoel wrote:
On 2011-01-30 17.08, ms wrote:
Since I have exactly the same needs (charged system in vacuum) I jump
in...
In http://www.gromacs.org/Documentation/Errors
it says:
Note for PME users: It is possible to use a uniform neutralizing
background charge in
On 2011-01-30 17.08, ms wrote:
On 30/01/11 15:41, David van der Spoel wrote:
My question is what effect does running a simulation with a charged
system have? I recall reading that something related to PME
calculations assumes the system is neutral, but it did not specify
whether it was referrin
On 30/01/11 15:41, David van der Spoel wrote:
My question is what effect does running a simulation with a charged
system have? I recall reading that something related to PME
calculations assumes the system is neutral, but it did not specify
whether it was referring to MD or EM. From the mailing
On 2011-01-30 16.02, ms wrote:
On 29/01/11 05:08, Matt Chan wrote:
Perfect. This is great reading.
Thanks for the pointers Mark.
Matt
On 01/28/2011 06:50 PM, Mark Abraham wrote:
On 29/01/2011 9:57 AM, Matthew Chan wrote:
Hi,
I'm a first time GROMACS user. I've got 2 questions, which I'll
On 29/01/11 05:08, Matt Chan wrote:
Perfect. This is great reading.
Thanks for the pointers Mark.
Matt
On 01/28/2011 06:50 PM, Mark Abraham wrote:
On 29/01/2011 9:57 AM, Matthew Chan wrote:
Hi,
I'm a first time GROMACS user. I've got 2 questions, which I'll ask
in separate emails. The firs
Perfect. This is great reading.
Thanks for the pointers Mark.
Matt
On 01/28/2011 06:50 PM, Mark Abraham wrote:
On 29/01/2011 9:57 AM, Matthew Chan wrote:
Hi,
I'm a first time GROMACS user. I've got 2 questions, which I'll ask
in separate emails. The first is about running EM on a charged
p
On 29/01/2011 9:57 AM, Matthew Chan wrote:
Hi,
I'm a first time GROMACS user. I've got 2 questions, which I'll ask in
separate emails. The first is about running EM on a charged protein in
vacuum.
I'm presently walking through some of the tutorials and trying to
simplify them for my purpose
On 18/01/2011 3:12 PM, bharat gupta wrote:
Sir,
That's what I want to know how u found out that the P.E. is ok and
then what about the PE graph ??
A value of large magnitude and negative sign is probably OK. Exactly how
large varies widely with system composition, force field, etc. So nobody
Sir,
That's what I want to know how u found out that the P.E. is ok and then
what about the PE graph ?? Does it has to be some what parallel to x-axis in
case of every minimized structure as in my case its not parallel to x-axis
, rather its getting down towards the x-axis.. ... generally for a m
On 18/01/2011 2:50 PM, bharat gupta wrote:
Hi,
I did the energy minimization of my protein (230 amino acids) after
adding ions .. and after checking the potential energy of the system I
was getting thee graph which is different from the one given in the
lysozyme tutorial i.e. the the potentia
bharat gupta wrote:
The potential energy graph is not coming parallel to x-axis is getting
down towars the x-axis .. normally it should be paralle to x-axis..
Depending on how quickly the potential energy converges, it may or may not. The
most important outcome of EM is that you achieve
Check your log file to see if the minimization criterion was satisfied ie
the max force is less than emtol.
On Mon, Jan 17, 2011 at 12:29 AM, bharat gupta wrote:
>
> The potential energy graph is not coming parallel to x-axis is getting down
> towars the x-axis .. normally it should be paralle to
The potential energy graph is not coming parallel to x-axis is getting down
towars the x-axis .. normally it should be paralle to x-axis..
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National
OK what seemed wrong to you?
On Mon, Jan 17, 2011 at 12:24 AM, bharat gupta wrote:
> I am doin the first minimization step.. here are the details of minim.mdp
> file
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
I am doin the first minimization step.. here are the details of minim.mdp
file
; 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 = 1000.0 ; St
Can you provide more details ? Which graph are you talking about ?
Amit
On Mon, Jan 17, 2011 at 12:05 AM, bharat gupta wrote:
> Hi all,
>
> I am minimizing my protein (230 amino acids) with the minim.mdp file given
> in the lysozyme tutorial but I am not getting a stable graph .. I checked
> th
Nikhil,
I had a similar problem, and was getting the same error. In my case the order of my atoms was different in my pdb/gro and my top/itp file. This made my system do a weird inversion, due to incorrect placement of atoms. And my energies were terrible.
Look at atom 1149, exactly as the error message has noted.
Is it, or any of it's neighbours, not quite where it "should" be?
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
- Original Message -
From: priyabrata panigrahi
Date: Thursday, August 26, 2010 17:09
Subject: [gmx-users] Energy minimization by keeping heavy atom fixed
To: gmx-users@gromacs.org
> I have a protein structure determined by x-ray crystallography method where
> hydrogen atoms were missi
The implicit water models were built in a time when computing time was limiting
because of the computing power if this epoch. But now is feasible to do
simulations with explicit water. Maybe one should argue that at the first
minimization of a protein waterbox the waters are not in the natural posi
>
> Without having actually read their paper... there's could easily be a kind
> of apples-and-oranges comparison going on. The local optimum resulting from
> a single EM using MM forcefields optimized for non-vacuum conditions on
> near-native folds in vacuo are being compared with (say) crystal s
- Original Message -
From: Thomas Evangelidis
Date: Thursday, June 17, 2010 10:48
Subject: [gmx-users] Energy minimization: problems with ramachanrad score
To: gmx-users@gromacs.org
> I 'm trying to relax my homology models from steric clashes, and while
> searching for the appropriate m
On 8/04/2010 4:23 PM, Evelyne Deplazes wrote:
Hi gmx-users
I am somehow famliar with gromacs but only used it with coarse grained
force fields (Martini) so far, not with all atom ones. I am now trying
to run a simulation on a membrane protein system (protein embedded in a
POPC bilayer solvated w
What are the atoms that are causing the problems actually doing, where are they
located etc?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+
Ozge Engin wrote:
Hi all,
I have been trying to calculate the PMF of two NA+ ions in explicit bulk
water. First, I tried to calculate the mean force between the two ions
at a distance of 0.48 nm, which is big enough than the diameter of the
ions. I first energy minimized the system with the
shahab shariati wrote:
Hi gromacs users
I want to study interaction of protein-dna by gromacs.
For energy minimization, is using of only 1 algorithm, for example
steepest descent or conjugate gradient, enough? How many steps is
necessary for EM?
I would encourage you to do some backgrou
Actual text input / output would be a good idea here. What is the actual
output when you try to run it the second time?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dall
ad of just trying to find a way to
push forward.
-Justin
^
^subarna
*From:* Mark Abraham
*To:* Discussion list for GROMACS users
*Sent:* Thu, 10 December, 2009 2:33:23 PM
*Subject:* Re: [gmx-users] energy minimiz
Hello
Can increase the emtol from 1000 to 1 KJ mol - 1 nm-1?
subarna
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Thu, 10 December, 2009 2:33:23 PM
Subject: Re: [gmx-users] energy minimization
subarna thakur wrote:
> I am doing
subarna thakur wrote:
I am doing the energy minimization of a protein using the following
keywords in em.mdp file-
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 3000
;
;Energy minimizing s
leila karami wrote:
Hi
I want to do energy minimization but follow subject is came up:
writing lowest energy coordinates.
Back Off! I just backed up ooo.gro to ./#ooo.gro.5#
Steepest Descents did not converge to Fmax < 2000 in 101 steps.
Potential Energy = -3.2421097e+05
Maximum force =
Hi Leila,
Where does it say that you encountered an error?
You also could've checked the wiki/mailing lists for this and found
that this is normal and sufficient for starting an MD simulation.
Cheers,
Tsjerk
On Wed, Nov 11, 2009 at 9:10 AM, leila karami wrote:
> Hi
>
> I want to do energy mini
David Crosby wrote:
Hello all, how are you doing today?
I've been trying to get a stable DNA MD simulation to work for me, but I
think my problem lies in an insufficiently energy minimized system prior to
running the pr step. I'm using the ffamber99 force field and I've
successfully simulated
leila karami wrote:
how can I do energy minimization with position restraint. how I creat
cooresponding mdp file? what should considered except what is seen in
below mdp file.
Reading the manual, wiki, and the many tutorials available will give you the
background you need. The obvious qu
Apart from specifying -DPOSRES in your mdp file, you need to make sure that
posre.itp will be included into your topology. There is usually a statement
like 'ifdef POSRES ..."
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf
Jamie Seyed wrote:
Dear all, Thanks for all comments. I will check again all steps for my
previous simulation with right files (according to Mark) and then I will
let you know if I got the same problem (I am not working on proteins).
Another question:
--After energy minimization step for in-v
Dear all, Thanks for all comments. I will check again all steps for my
previous simulation with right files (according to Mark) and then I will let
you know if I got the same problem (I am not working on proteins).
Another question:
--After energy minimization step for in-vacuo run, Should I do sti
Hi,
On Wed, Aug 12, 2009 at 3:06 AM, Mark Abraham wrote:
> Jamie Seyed wrote:
>>
>> Dear all,
>> I performed an md simulation but it crashed at the beginning because
>> according to it "system was exploding". Also when I tried to see the
>> system
>> by ngmx, there was no water anymore and it was
Jamie Seyed wrote:
Dear all,
I performed an md simulation but it crashed at the beginning because
according to it "system was exploding". Also when I tried to see the system
by ngmx, there was no water anymore and it was only the molecule sitting in
the box(after grompp and before mdrun it was a
Jamie Seyed wrote:
Dear all,
I performed an md simulation but it crashed at the beginning because
according to it "system was exploding". Also when I tried to see the
system by ngmx, there was no water anymore and it was only the molecule
sitting in the box(after grompp and before mdrun it w
Thank you so much for all the helpful response.
On Wed, May 6, 2009 at 4:59 PM, Mark Abraham wrote:
> Yanmei Song wrote:
>
>> Dear All:
>>
>> I just installed the gmx_4.0.4 double precision.
>>
>> When I do EM, the grompp_d command has no problem. However after I submit
>> the job, it gives me t
Yanmei Song wrote:
Dear All:
I just installed the gmx_4.0.4 double precision.
When I do EM, the grompp_d command has no problem. However after I
submit the job, it gives me the following error. Anyone can tell me what
is the problem which may cause that?
You're using a new .tpr with an o
Justin A. Lemkul wrote:
Yanmei Song wrote:
Dear All:
I just installed the gmx_4.0.4 double precision.
When I do EM, the grompp_d command has no problem. However after I
submit the job, it gives me the following error. Anyone can tell me
what is the problem which may cause that? By the
Yanmei Song wrote:
Dear All:
I just installed the gmx_4.0.4 double precision.
When I do EM, the grompp_d command has no problem. However after I
submit the job, it gives me the following error. Anyone can tell me what
is the problem which may cause that? By the way, in 4.0.4, it can only
Q. Y. HUAN wrote:
Hi all,
Is it right if running energy minimization using 4 nodes?
Yes.
Mark
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Quoting prasun kumar <[EMAIL PROTECTED]>:
> dear users ,
> while doing energy minimization I am getting warning as following
>
> 1-4 interaction between 3154 and 3163 at distance 2.109 which is larger than
> the 1-4 table size 1.000 nm
This is one of the most common questions on the list. You've
> Also, I still have an issue with how Gromacs is building my system. when I
> run
> editconf -f $protName.gro -o box.gro -d 1.2 -bt dodecahedron
> Gromacs places the solute in the top corner of the box, rather than
> centering it in the box. Shouldn't it be in the center? What am I doing
> wron
On Sat, 26 Jan 2008 21:40:20 -0800
Patricia Francis-Lyon <[EMAIL PROTECTED]> wrote:
I want to do energy minimization on a loop that had been missing and was
filled in by modloop, while freezing the rest of the protein.
Before the minimization I have an SO4 ion and 135 water molecules from t
Ananya Debnath wrote:
Hi,
I am a recent user of Gromacs. I tried to make initial configuration
of a bilayer in united atom model having Btmac, Stearyl alcohol and
water with packmol and then energy minimization with gromacs.
Initially I made a bilayer with gromos87 forcefield, ffgmx.itp, and
tha
Hi,
How about trying md with very small step size such as
dt = 0.0001
?
Once I had similar problem like you and it is solved by performing
additional energy minimization step with very small step size.
I can't guarentee this method, but I think it might be OK.
On 8/13/07, Q733 <[EMAIL PROTECTED
There's probably a problem either with your structure or your topology. Spend
some time looking at what you've done. I'd start by investigating atom 483.
It should be pretty obvious what's wrong, with a force like that.
- Original Message
From: Q733 <[EMAIL PROTECTED]>
To: gmx-users@
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