I often use 4 fs with all-bonds and virtual sites, especially if lacking
sampling is a greater source of error than the kinetic energy being slightly
off.
Erik
On 15 Aug 2013, at 20:58, Michael Shirts mrshi...@gmail.com wrote:
I don't go beyond 2 fs with either all- bonds or h-bonds. Things
I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic
energy start being subtly off.
H-bonds has less chance of failing with large numbers of constraints- less
iteration required, especially if bond system cross parallelization boundaries.
If your molecules are 10
On 5/14/13 10:27 AM, Joe Smerdon wrote:
Hi all,
First of all I'm new to md simulations, so if I am missing anything simple, I
would be grateful for any pointers, however small. I am trying to simulate
many small molecules on a substrate. I am restraining my substrate from moving
but
I wouldn't call 8ps late. Since you probably don't know how large a time
step is safe, I'd try 0.1 fs for equilibration, and raise it later if it
proves stable.
Mark
On May 14, 2013 4:28 PM, Joe Smerdon jsmer...@uclan.ac.uk wrote:
Hi all,
First of all I'm new to md simulations, so if I am
On 1/1/13 8:56 AM, Shima Arasteh wrote:
Hi,
I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD
simulation following the Justin's tutorial of kalp15-DPPC.
The force field which I use, is charmm36.
In NVT step, I get LINCS-warning as follow:
Step 0, time 0 (ps)
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Tuesday, January 1, 2013 6:45 PM
Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 8:56 AM, Shima
On 1/1/13 10:41 AM, Shima Arasteh wrote:
Thanks.
I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference
I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER
was constraints = h-bonds , however it was
, January 1, 2013 7:17 PM
Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 10:41 AM, Shima Arasteh wrote:
Thanks.
I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER
systems. The only difference I found between them was about the bonds
constraints
On 1/1/13 10:53 AM, Shima Arasteh wrote:
If I tell you that I changed the constraints and now the NVT is running,
would that be ok? However I don't know the scientific reason of this incident!
But I bring you the EM.mdp as follow:
define = -DSTRONG_POSRES
integrator= steep
Thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Tuesday, January 1, 2013 7:27 PM
Subject: Re: [gmx-users] LINCS WARNING - Protein
On 10/12/12 2:42 AM, tarak karmakar wrote:
Dear ALL,
In my protein I need to constraint the length between the Metal and
the N of Histidine residues. In the .rtp file I didn't specify this
Mn-N connectivity; these are more or less coordinate bonds. So to do
that I specified the Mn, N-atom
On 10/1/12 7:10 AM, Ali Alizadeh wrote:
Dear all users
1- I am trying to simulate a system that contains 1182 methane
molecules(5910 atoms) and 1830 water molecules(5490), I
keep getting these errors.
Something is wrong with the starting configuration, topology, or .mdp settings
(see
Hi,
now I tried it without any restriction and still the LINCS warnings occur.
Since it is always the hydrogen atom where the huge force lies on I had
the idea just to remove the hydrogen atom to find out whether another atom
will occur to have such a high force on or everything went fine. And
On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
now I tried it without any restriction and still the LINCS warnings occur.
Since it is always the hydrogen atom where the huge force lies on I had
the idea just to remove the hydrogen atom to find out whether another
Hi Justin,
thank you a lot for your answer. I will try it.
Best,
Eva
On 9/20/12 6:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi,
now I tried it without any restriction and still the LINCS warnings
occur.
Since it is always the hydrogen atom where the huge force lies on I
I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
I just added the phosphate manually and so I want to minimize and run a
short MD with it.
I added the dihedraltype of the amber database
On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
I just added the phosphate manually and so I want to minimize and run a
short MD with it.
I added the dihedraltype of
Looks like there is still something clashing with atom 979.
The resulting force after EM was close to 1, which is not very much
minimized at all...
What is atom 979 and what is near it?
On 2012-09-18 01:22:25PM +0200, reising...@rostlab.informatik.tu-muenchen.de
wrote:
I need the rest of
On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
Another thing worth considering - why do you necessarily need the rest of the
structure to be identical? Or
Okey,
now I tried it without any fixed residues. But still the energy after the
minimization is not very low and I still get the LINCS warnings.
The mdp file I use for the minimization looks like this:
define = -DPOSRES
integrator = steep
emtol =
On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Okey,
now I tried it without any fixed residues. But still the energy after the
minimization is not very low and I still get the LINCS warnings.
The mdp file I use for the minimization looks like this:
define
On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
this atom is the CG atom of the phosphate I added to the protein.
But how can I find out by what it is punished?
Visualization.
This is the topology for this residue in the aminoacid.rtp file. I added
it
Ah okey. Thank you.
I will write them.
Hmm, but the protein is a crystal structure from pdb with a resolution of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md run. And there were no errors. And
now I only added the phosphate to the
On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ah okey. Thank you.
I will write them.
Hmm, but the protein is a crystal structure from pdb with a resolution of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md
On 9/12/12 6:57 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
during the mdrun_mpi I get many LINCS warnings like for example:
Step 1143, time 1.143 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.265373, max 1.416702 (between atoms 976 and 979)
Hi Justin,
my mdp file for the md run looks like this:
define = -DPOSRES
integrator = md
dt = 0.001
nsteps = 5000
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 500
nstenergy
On 9/12/12 3:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
my mdp file for the md run looks like this:
define = -DPOSRES
integrator = md
dt = 0.001
nsteps = 5000
nstxout = 100
nstvout = 0
nstfout
On 17/08/2012 2:02 PM, shahid nayeem wrote:
Dear all
One basic clarification. How does LINCS algorithm influences the results
of final production run. In what respect a minimization, pr and final
simulation done with constraints = none and with constraint= all_bonds are
different.
Sounds like
Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy minimization with setting constraint =
none, making it
On 17/08/2012 2:28 PM, shahid nayeem wrote:
Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy
I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
Shahid nayeem
On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 17/08/2012 2:28 PM, shahid
On 17/08/2012 2:56 PM, shahid nayeem wrote:
I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
All you can do is use pdb2gmx as you do for the normal termini. pdb2gmx
On 8/2/12 9:57 AM, Christian Blouin wrote:
My simulation aborts rather quickly because it accumulates too many
LINCS warning. I checked the various plots and everything seems to be
stable (temperature, pressure, total energy, etc.). The stderr gives
me warnings looking like this:
Step
Good question. Short answer, no -- LINCS doesn't play well with a
velocity verlet based pressure control algorithm.
Long answer: MTTK has ended up not being robust because you need to
solve a self consistent set of equations every timestep using the
pressure estimator, which is extremely noisy,
On 11/06/2012 4:38 PM, rama david wrote:
Hi Gromacs Friends ..
I am trying to simulate octa-peptide in water model spc using G96 53a6
force field.
my aim is to study the self assembly nature of these octapetide.
I did following type of arrangment.
I make antiparrallel arrangment of four
Hi MARK,
Thank you to your Quick reply,
Please accept my apology for incomplete information...
I did simulationm of single, Double and four peptide..
I also tried following
I make antiparrallel arrangment of four peptide with distance of 0.4 nm in
y direction,
Then I translate these layer in
On 11/06/2012 5:49 PM, rama david wrote:
Hi MARK,
Thank you to your Quick reply,
Please accept my apology for incomplete information...
I did simulationm of single, Double and four peptide..
I also tried following
I make antiparrallel arrangment of four peptide with distance of 0.4
nm in y
Hi Mark,
I did simulation of the same system in vacuum, and system behave the
normally,
So the instability in the system is due to the spc Water model???
As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up
I think the source is (Please tell me is it right..?? or any else
On 6/11/12 6:23 AM, rama david wrote:
Hi Mark,
I did simulation of the same system in vacuum, and system behave the normally,
So the instability in the system is due to the spc Water model???
As per the link http://www.gromacs.org/Documentation/Terminology/Blowing_Up
The water model is
Hi Justin, thank you for quick reply.
You are right I have practicle result, And I want to replicate them..
Thank you for your suggestion..
With Best Wishes,
Rama David
On Mon, Jun 11, 2012 at 3:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 6/11/12 6:23 AM, rama david wrote:
Hi
On 9/03/2012 4:27 PM, rama david wrote:
Hi GROMACS specialist,
I am using MARTINI forcefield,
My mdp file contain following parameter
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 90
gromacs output is
Step 0, time 0 (ps)
On 8/03/2012 5:05 AM, francesco oteri wrote:
Hi gromacs users,
I am tying to minimize a protein through grolacs 4.5.5 double precision.
If I try to minimize it without virtual site, everythin goes fine but
if I add virtual site through:
pdb2gmx -vsite hydrogens -chainsep id -f Aqui_model.pdb
vivek sharma wrote:
Hi There,
I was trying to run a equilibrium run (npt) for system of Methane in
1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF
parameters). Following is the series of steps I followed:
1. Energy minimization with steep integrator for 5000 steps
Hi Justin,
Thanks for your response. After posting my query, I tried running the
similar set with
NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p
= 0.5, compressibility = 4.5e-05, ref_p = 1.0)
On giving berendsen instead of Parrinello-Rahman for pressure
coupling, job
On 10/02/2012 4:41 PM, vivek sharma wrote:
Hi Justin,
Thanks for your response. After posting my query, I tried running the
similar set with
NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p
= 0.5, compressibility = 4.5e-05, ref_p = 1.0)
On giving berendsen instead of
On 20/01/12, Ben Porebski b...@inoxx.net wrote:
Hi all,
I've been working on some structures between 2.5A and 3.4A in resolution and
all of my structures suffer from lincs warnings.
From reading the page about lincs warnings, I've performed a more lengthy
equilibration:
I'm using
Ciao,
I've seen this behavior (something running fine on one core but
failing on multiple cores, or certain multiples of cores) frequently.
It's almost always due to an unstable system. Have your user try
equilibrating longer, or minimize with flexible water before trying
equilibration. You can
Thank for you answer. Meanwhile, our user told us that she found the
ideal configuration for running her simulations; nevertheless, i linked
her this discussion in case she can find some interesting suggestion.
Cheers,
Alessandro
Il 16/01/2012 16.05, Matthew Zwier ha scritto:
Ciao,
I've
I get an error like this=
Step 43230, time 86.46 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033583, max 1.621884 (between atoms 2032 and 2030)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2032 2030 90.0
aiswarya pawar wrote:
I get an error like this=
Step 43230, time 86.46 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033583, max 1.621884 (between atoms 2032 and 2030)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
On 19/12/2011 1:05 AM, aiswarya pawar wrote:
Hi users,
I did energy minimization of a protein complex using the following
minimization mdp file.
See
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
for general advice.
; Lines starting with ';' ARE COMMENTS
;
Yuri Garmay wrote:
Hi, all!
I am trying to simulate a system of peptide, water, NaCl and DMSO.
I used pdb2gmx to generate .top file for DMSO and then created this .itp:
(initial DMSO structure had been minimized before it was used for box
generation)
[ moleculetype ]
; Name
Try minimizing again now with all bonds constrained using the output of
the EM that ran. Generally, if EM crashes, your system contains some
unresolvable clash or inappropriate geometry. Perhaps you have now relaxed
the bad interactions sufficiently to proceed.
I had examined structure
On 1/11/2011 3:43 AM, Yuri Garmay wrote:
Try minimizing again now with all bonds constrained using the
output of the EM that ran. Generally, if EM crashes, your system
contains some unresolvable clash or inappropriate geometry.
Perhaps you have now relaxed the bad
Yun Shi wrote:
Hi all,
I want to do MD simulation with amber99SB force field, which I found
originally developed using SHAKE algorithm to constrain all bonds
involving hydrogen atoms. But it seems to me that SHAKE is still not
supported with domain decomposition in GROMACS4.5.4, and we can
On 4/30/2011 9:06 AM, Juliette N. wrote:
Dear experts,
I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few
steps I get LINCS error:
step 400, will finish Sat Apr 30 05:20:45 2011
Step 750, time 1.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms
On 23/03/2011 9:45 PM, Anna Marabotti wrote:
Dear gmx-users,
I'm experimenting a LINCS warning on my system, an enzyme with ATP,
galactose and Mg. We started from the crystallographic structure, made
some accommodation on the topology of the sugar in order to check for
partial charges
Hello Justin,
Thanks for you reply. My late response is because I have been trying to
resolve the problem.
Dear experts,
I am trying to build up a polymer in hexane system by increasing the
density. After PR step, my NVT and NPT trailes failed. Initially I used to
get LINCS and 1-4 warnings
Moeed wrote:
Hello Justin,
Thanks for you reply. My late response is because I have been trying to
resolve the problem.
Dear experts,
I am trying to build up a polymer in hexane system by increasing
the density. After PR step, my NVT and NPT trailes failed.
Moeed wrote:
Dear experts,
I am trying to build up a polymer in hexane system by increasing the
density. After PR step, my NVT and NPT trailes failed. Initially I used
to get LINCS and 1-4 warnings (even for NVT) which were not because of
flawed topology file. It turned out that
On 16/03/11, Moeed lecie...@googlemail.com wrote:
Dear experts,
I am trying to build up a polymer in hexane system by increasing the density.
This seems to have been taking months. Why aren't you using genbox on your
polymer starting configuration and an equilibrated box of hexane of
Thank you! I will try to change something and write to you about the result
.
--
Sincerely,
Yulian Gavrilov
--
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Please search the archive at
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zeppelin zeppelin wrote:
Dear GROMACS users,
I only begin to work with gromacs and now have some problems with tetra
protein.
I used AMBER force field and made several changes (in ffamber.rtp,
specbond.dat, ffamber99bon.itp) to create an isopeptide bonds between
monomers.
Minimization and
Raymond.nuist wrote:
Dear users
Here is my problem:
I just changed my GMX version from 4.0 to 4.5.
But the task was in a Segmentation fault, whileI can mdrun it
well in 4.0 environment .
Providing an .mdp file and a description of your system would be useful.
Yes, I understand that. But then this is a protein in water simulation with
CHarmm forcefield and I cannot find a reason as to why does this happen(esp
after variable number of steps)? I have checked the .pdb files generated for
the steps where Lincs fails and it seems that H atoms for atleast 1
Sai Pooja wrote:
Yes, I understand that. But then this is a protein in water simulation
with CHarmm forcefield and I cannot find a reason as to why does this
happen(esp after variable number of steps)? I have checked the .pdb
files generated for the steps where Lincs fails and it seems that
- Original Message -
From: Sai Pooja saipo...@gmail.com
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users gmx-users@gromacs.org
Yes, I understand that. But then this is a protein in water simulation with
CHarmm
-
From: Sai Pooja saipo...@gmail.com
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users gmx-users@gromacs.org
Yes, I understand that. But then this is a protein in water
simulation with CHarmm forcefield and I cannot find a reason
: Sai Pooja saipo...@gmail.com
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users gmx-users@gromacs.org
Yes, I understand that. But then this is a protein in water simulation
with CHarmm forcefield and I cannot find a reason as to why
- Original Message -
From: Sai Pooja saipo...@gmail.com
Date: Monday, November 1, 2010 10:24
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users gmx-users@gromacs.org
Some information:
Except for this note, I do not get any other warning when I generate
cannot handle.
Quoting Mark Abraham mark.abra...@anu.edu.au:
- Original Message -
From: Sai Pooja saipo...@gmail.com
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users gmx-users@gromacs.org
here.
Quoting Mark Abraham mark.abra...@anu.edu.au:
- Original Message -
From: Sai Pooja saipo...@gmail.com
Date: Monday, November 1, 2010 10:24
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users gmx-users@gromacs.org
Some information:
Except
Abraham mark.abra...@anu.edu.au:
- Original Message -
From: Sai Pooja saipo...@gmail.com
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users gmx-users@gromacs.org
Yes, I understand
Sai Pooja wrote:
For Replica exchange, is there any advantage of in using SHAKE over
LINCS(other than the stepsize)?
I am running an REM simulation and the simulation stops after running
for variable number of steps (10, 1000 etc.) because some bond
moves more than 30 degrees and
On 31/10/2010 10:04 AM, chris.ne...@utoronto.ca wrote:
Justin is probably correct, your system is unstable. However, let me
mention another possibility. As the temperature increases, the largest
stable timestep decreases in length. Is it possible that over some
temperature (1000K?) a 2 fs
I would look for an error in the input files first.
However, I have a suspicion that this artifact is most likely from a
thermostat problem than LINCS. LINCS may be the object that is
throwing the exception, but in a recent paper by Rosta et.al., it was
shown that weak-coupling thermostats
Moeed wrote:
Dear gmx experts,
I am having problem doing MD run for a hydrocarbon system. The system
contains a stack of Hexane molecules using editconf.
The distance between molecuels in the box is more than 30 A. I am
wondering why I get large forces (system is blowing up) with this
Hi,
So many posts and replies on a single issue, and still no exact
command lines, nor grompp output, nor gromacs version. Lin, please be
aware that such errors only make sense in the context of what you did.
You'll have to provide all information that might be related to it.
I'm pretty sure that
Chih-Ying Lin wrote:
Hi
what does the max max 597108032.00 (between atoms 366 and 368) mean?
is it the max force or max length of the system?
where is the max force listed?
Don't know.
max 597108032.00 (between atoms 366 and 368) rms 26394490.00
bonds that rotated more than 30
Chih-Ying Lin wrote:
Hi
what does the max max 597108032.00 (between atoms 366 and 368) mean?
is it the max force or max length of the system?
where is the max force listed?
It corresponds to the length between the constrained atoms. Forces are printed
to the .trr file if you have
Yongchul Chung wrote:
Hi again gmx-users,
I ran into LINCS error again when I tried to incorporate pressure
scaling parameters.
It seems like the initial pressure and temperature is erroneously large
as shown in the md.log file below. can anyone tell me how to fix this?
Did you run
Yongchul Chung wrote:
yes I carried out energy minimization and used following parameters.
OK, so what values of potential energy and maximum force did EM achieve?
-Justin
title = FWS
cpp = /usr/bin/cpp ; the c pre-processor
define =
After EM, I got:
Potential Energy = 1.7242092e+05
Maximum force = 2.1079963e+03 on atom 675
Norm of force = 5.9417034e+01
I think my system size is too big compared to the box size so I am going to
run the simulation with smaller number of molecules to see whether this
helps or not.
Yongchul Chung wrote:
After EM, I got:
Potential Energy = 1.7242092e+05
Maximum force = 2.1079963e+03 on atom 675
Norm of force = 5.9417034e+01
I think my system size is too big compared to the box size so I am going
to run the simulation with smaller number of molecules to see
delta_t = 0.01
You are using a 10 fs timestep!!! That is way too long. Standard is 2
(with bond constraints).
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I
Hi guys,
As Justin pointed out, it was the problem with md simulation blowing up. I
also had coloumbtype=PME and had to switch to cut-off to make my simulation
run faster.
Thanks for all the help.
On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub joc...@xray.bmc.uu.se wrote:
delta_t
Yongchul Chung wrote:
Hi guys,
As Justin pointed out, it was the problem with md simulation blowing up.
I also had coloumbtype=PME and had to switch to cut-off to make my
simulation run faster.
And it will be substantially less accurate than using PME. I would say Jochen's
advice is
sunny mishra wrote:
Hi,
I have a quick question. My system exploded when I tried to run the
simulation and it gives me the LINCS warning. I am using MARTINI
forcefield and finally I get segmentation fault. I don't know that what
are the factors do i need to change to get rid of the LINCS
sunny mishra wrote:
Hi Justin,
Thanks for the reply. I am doing the energy minimization of Na K pump
with PDB ID 3B8E using MARTINI forcefield. Here is my em.mdp file for
the same. First I get the .gro file from my cleaned PDB file and then
try to minimize the system using grompp and then
Hi Justin,
Thanks for the reply. I am doing the energy minimization of Na K pump with
PDB ID 3B8E using MARTINI forcefield. Here is my em.mdp file for the same.
First I get the .gro file from my cleaned PDB file and then try to minimize
the system using grompp and then when I do mdrun it gives me
On 08/28/09, tekle...@ualberta.ca wrote:
Hi Justin,
There is something physically unrealistic about your model
You are right!
The main problem I found out is that some of the structures in my Solution
broke down..
I used ...
genbox -cp .grob -nmol 20 -ci insert.gro -cs
Hi,
.snip...
No, because that's not a well-defined proposition. You could generate a
small box with one solute +solvent, and then use *genbox* to replicate it.
genconf, rather than genbox:
genconf -f in.gro -o out.gro -nbox nx ny nz
with suitable nx, ny and nz for nx*ny*nz copies.
Hi Justin,
There is something physically unrealistic about your model
You are right!
The main problem I found out is that some of the structures in my
Solution broke down..
I used ...
genbox -cp .grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top
-XX.gro
To generate
tekle...@ualberta.ca wrote:
Hi Justin,
There is something physically unrealistic about your model
You are right!
The main problem I found out is that some of the structures in my
Solution broke down..
I used ...
genbox -cp .grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top
Hi Justin,
I tried to run full MD after energy minimization in both vacuo and
water... went good but I got this ERROR once I try to run full MD.
Can you please help.
=
Step 0, time 0 (ps) LINCS WARNING
relative constraint
tekle...@ualberta.ca wrote:
Hi Justin,
I tried to run full MD after energy minimization in both vacuo and
water... went good but I got this ERROR once I try to run full MD.
Can you please help.
There is something physically unrealistic about your model. That's the case
whenever you
Samik Bhattacharya wrote:
Hi all, i ma simulating a membrane protein, in which i am facing a
problem in the equilibration step. in the NVT equilibration when i am
running the mdrun command i am getting a msg like
Program mdrun, VERSION 4.0.5
Source code file: constr.c, line: 136
Fatal error:
--- On Wed, 15/7/09, Mark Abraham mark.abra...@anu.edu.au wrote:
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] Lincs Warning
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Wednesday, 15 July, 2009, 5:23 PM
Samik Bhattacharya wrote:
Hi all, i ma
Samik Bhattacharya wrote:
--- On *Wed, 15/7/09, Mark Abraham /mark.abra...@anu.edu.au/* wrote:
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] Lincs Warning
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Wednesday, 15 July, 2009, 5:23
--- On Thu, 16/7/09, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Lincs Warning
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Thursday, 16 July, 2009, 7:30 AM
Samik Bhattacharya wrote:
--- On *Wed, 15/7/09
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