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) LINCS WARNING
relative constraint deviation
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 10/1/12 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
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)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous,
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
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
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
2. Energy minimization with
Dear all,
I am trying to simulate a GB simulation of a 112 amino acid long protein. I
keep getting these errors,
Step 27718, time 55.436 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 33.319842, max 438.763717 (between atoms 79 and 81)
bonds that rotated more than 30 degrees:
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 (according to Justin Lemkul's suggestions on PRODRG
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
Thank you! I will try to change something and write to you about the result
.
--
Sincerely,
Yulian Gavrilov
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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 equilibration (NPT and NVT) were
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
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 .
Here is the error:
Step 1902, time 1.902 (ps) LINCS WARNING
relative constraint deviation
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.
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 distance!. (LINCS
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
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?
max 597108032.00 (between atoms 366 and 368) rms 26394490.00
bonds that rotated more than 30 degrees:
what does previous, current
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
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:
Too many LINCS warnings
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
Maximum force = 4.9815813e+24 on atom 169274
You should have a look at that atom, that is a large force.
___
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Please search the archive at
Dears,
I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.
After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs warnings.
When restarting the simulation feeding -cpi md.cpt to mdrun
XAvier Periole wrote:
Dears,
I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.
After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs warnings.
When restarting the simulation feeding
On Jun 3, 2009, at 9:51 AM, Mark Abraham wrote:
XAvier Periole wrote:
Dears,
I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32 CPUs.
After some ns lincs warnings appear and eventually the simulation
crashes dues
to too many lincs
Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,
large time steps and a system that probably wasn't equilibrated enough.
Ran.
XAvier Periole wrote:
Dears,
I am experiencing some problems running a few proteins in water
(GROMOS43a1/SPC)
with gmx-4.0.4 using 32
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:
Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,
No virtual sites.
large time steps and a system that probably wasn't equilibrated
enough.
time step 2 fs and a system totally equilibrated, nothing there.
I
XAvier Periole skrev:
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:
Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,
No virtual sites.
large time steps and a system that probably wasn't equilibrated enough.
time step 2 fs and a system totally equilibrated,
On Jun 3, 2009, at 10:58 AM, Giovanni Bussi wrote:
Dear Xavier,
With the default flag for pbc (periodic_molecules=no) you may end up
in lincs problem if an atom of the protein becomes too close to the
image of another atom of the protein.
If this is your case, use periodic_molecules=yes, or
On Jun 3, 2009, at 10:48 AM, Erik Marklund wrote:
XAvier Periole skrev:
On Jun 3, 2009, at 10:01 AM, Ran Friedman wrote:
Hi XAvier,
Do you use virtual sites? I've seen this when I used virtual sites,
No virtual sites.
large time steps and a system that probably wasn't equilibrated
Hi!
I am getting a message in the MD log file as below with respect ro LINCS
mentioning deviations. I have constrained all bonds but this problem seems
to pertain to a water molecule. Please suggest a way to oversome this issue.
Thanks
Jayant James
Initializing LINear Constraint Solver
number of
Dear all,
I am making drg+lipid simulations with gmx. From the 9 series of experiments
all of them worked fine for 250 ps equilubration run. However, when I start the
real simulation, 4 of them stopped after 300 ps (I have setted the simualtion
time to 2.5 ns). It complains the LINCS warning.
serdar durdagi wrote:
Dear all,
I am making drg+lipid simulations with gmx. From the 9 series of
experiments all of them worked fine for 250 ps equilubration run.
However, when I start the real simulation, 4 of them stopped after 300
ps (I have setted the simualtion time to 2.5 ns). It
Hellow :
I am runing a MD of protein. Now I see some warning message on screen,I
don't
know how to understand it , Could somebody tell me about it? Thank you very
much!
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
931932 33.0
I am runing a MD of protein. Now I see some warning
message on screen,I don't know how to understand it , Could
somebody tell me about it? Thank you very much!
It means that the bond between the two atoms listed there is moving too
far in each time step. The reason for that problem can
Qiang Zhong wrote:
Hellow :
I am runing a MD of protein. Now I see some warning message on screen,I
don't
know how to understand it , Could somebody tell me about it? Thank you very
much!
First, consider what LINCS does. Then consider what could make LINCS
unhappy with the
Dear all,
I have a query,
1. Are two trajectories comparable if each one of them
has been run in a different version of gromacs? Eg,
v3.2 and v3.3.
Thanks in advance,
Regards,
Raghu
**
Y. M. Ragothaman,
Research Scholar,
Centre for Computational Biology and
Dear all,
I have a query,
1. Are two trajectories comparable if each one of them
has been run in a different version of gromacs? Eg,
v3.2 and v3.3.
Define comparable. If you mean are they sampling the same thermodynamic
ensemble, then the answer is yes if you used the same algorithms. If you
Hi everyone,
I'm having trouble with performing 1 ns simulations on a 318 residue
long protein with 'mdrun'. The run.log file, included at the end of
this message, gives a 'LINCS warning' within a minute or two after
the simulation begins:
Step 148, time 0.296 (ps) LINCS WARNING
relative
Hi everyone,
I'm having trouble with performing 1 ns simulations on a 318 residue
long protein with 'mdrun'. The run.log file, included at the end of
this message, gives a 'LINCS warning' within a minute or two after
the simulation begins:
Step 148, time 0.296 (ps) LINCS WARNING
relative
Dear all,
I am running the simulated annealing for a protein solvented in a water box,
but I get such LINCS WARNING as max 2022834176.00 (between atoms 5655 and 5658) rms 81089176.00
Why? Does it mean that my system is exploring?
The following is my mdp file and some of the LINCS
HiAttached is part of the gro file which gave the LINCS error on atoms. Thisoutput is the gro file for the initial mdrun, after which final grompp andfinal mdrun was done, which gives the error I described in the message
below.Gaurav Gaurav Chopra wrote: Hi I am getting the following error with
Hi
I am getting the following error with mdrun. I have done a few things
but the system complains of 1-4 interactions and gives LINCS warning if
the constraints are not turned off
in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in
ffoplsaa.itp and then did mdrun but I get 1-4
Gaurav Chopra wrote:
Hi
I am getting the following error with mdrun. I have done a few things
but the system complains of 1-4 interactions and gives LINCS warning if
the constraints are not turned off in the mdp file. I also changed the
fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then
On Mon, 17 Apr 2006 00:07:29 -0700
Gaurav Chopra [EMAIL PROTECTED] wrote:
Hi
I am getting the following error with mdrun. I have done
a few things but
the system complains of 1-4 interactions and gives LINCS
warning if the
constraints are not turned off in the mdp file. I also
changed the
Hello, gmx-users，
i am just simulating a single PEO chain in a large box(vacuum), the
EM step went perfectly well for steep and cg, but after MD has started there
came the following warnings:
Step 1432, time 2.864 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max
Hi
I get the following error when using mdrun for a protein in solution. I
have checked the structure and everything looks fine to me. Could you
suggested anything else I could do.
Step -2, time -0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.126305 (between atoms
Gaurav Chopra wrote:
Hi
I get the following error when using mdrun for a protein in solution.
I have checked the structure and everything looks fine to me. Could
you suggested anything else I could do.
Step -2, time -0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max
Gaurav Chopra wrote:
Hi
I get the following error when using mdrun for a protein in solution.
I have checked the structure and everything looks fine to me. Could
you suggested anything else I could do.
How did you energy minimze your structure? What was the output of mdrun
during energy
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