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 wrote:
> I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic
> e
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 atom
Searching through this mailing list it seems like some have stated that
with a 2 fs timestep (dt=0.002), constraints=h-bonds is fine in general.
The questions I have are:
1) What are some personal opinions on when it is ok to switch to h-bonds
from all-bonds for LINCS constraints? Is 2 fs an
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" wrote:
>
> Hi all,
>
> First of all I'm new to md simulations, so if I am missing anythin
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 allo
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 allowing the molecules to do whatever they like.
Thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Tuesday, January 1, 2013 7:27 PM
Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 10:53 AM, Shima Arasteh wrote
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
day, 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
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 "
the EM?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
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 Arasteh wrote:
> Hi,
>
&g
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) LINC
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 af
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 in
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 belo
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
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,
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
ind
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
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 = 1
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 perhaps
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 t
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
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
(http://personalpages.manchester.ac.uk/staff/Richard.Bryc
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 ru
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 minim
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 ma
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?
This is the topology for this residue in the aminoacid.rtp file. I added
it manually. The parameter are from the amber parameter database
(http://www.pharmacy.manchester.ac.
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
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 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)
bon
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, curre
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
-cha
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 wrote:
> On 17/08/2012 2:28 PM, shahid nayeem wrote:
>>
>> Rig
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 minimization
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 com
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
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.
> Shahid Nayeem
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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 2304252,
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 2304252, time 4608.5 (ps) LINCS WARNING
relative const
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, s
Hi all -
Is there any plan to get LINCS working with the MTTK barostat in the near
future?
Thanks
Katie
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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 wrote:
>
>
> On 6/11/12 6:23 AM, rama david wrote:
>
>>
>> Hi Mark,
>>
>>
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 no
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 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,
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 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 pepti
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 peptide with distance of 0.5 nm in
y direction,
Th
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) L
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) LINCS WARNING
relative constraint deviation
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
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 -ff charmm27
-water tip3p -posrefc 1000 -v -rtpr
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 Parrine
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 finished
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 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
On 20/01/12, Ben Porebski 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 grom
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 gromacs 4.0.7 single precision and the G53a6 force field with s
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 seen
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
Dear users,
I would like to ask your help about understanding a problem i'm not able
to recognize by myself.
Basically, a user of our sistem (IBM SP6, power6 architecture) is trying
to run a simulation of a very simple sistem, a polymer chain in a lot of
water molecules. While the simulation wo
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
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 90.00.44
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
; Ev
Hi users,
I did energy minimization of a protein complex using the following
minimization mdp file.
; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment
title = Energy Minimization ; Title of run
; The following line tell the program the standard locations where to
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 interactions
>
> 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 struct
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 ]
; Namenrexc
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 ]
; Namenrexcl
DMSO 3
[
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
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 only use LINCS for bon
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:
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 10.116560,
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 10.116560, max 72.359520 (between atoms 314 and 315)
bo
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 (accordi
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 server
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.
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 w
On 16/03/11, Moeed 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 the right
density?
M
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 simulations
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 simulations crashed just becaus
Thank you! I will try to change something and write to you about the result
.
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Sincerely,
Yulian Gavrilov
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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 e
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 O
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 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
Dear All,
About the Lincs warnings in Christoph Meier’ problem, is there any improved
method or a better way to deal with them? What we can do is to use shorter
timesteps or re-start the simulation using a frame before the first lincs
warning?
[gmx-users] LINCS Warnings in the middle of an
To be honest, I see the difference in your management of
protein and solvent temperatures as the biggest problem here.
Quoting Mark Abraham :
- Original Message -
From: Sai Pooja
Date: Monday, November 1, 2010 10:24
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list fo
vent temperatures as the biggest problem here.
>
>
>
> Quoting Mark Abraham :
>
>
>>
>> - Original Message -
>> From: Sai Pooja
>> Date: Monday, November 1, 2010 10:24
>> Subject: Re: [gmx-users] LINCS vs SHAKE
>> To: Discussion list for GR
ely, though. To be honest, I see the
difference in your management of protein and solvent temperatures as
the biggest problem here.
Quoting Mark Abraham :
- Original Message -
From: Sai Pooja
Date: Monday, November 1, 2010 10:24
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Disc
- Original Message -
From: Sai Pooja
Date: Monday, November 1, 2010 10:24
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users
> Some information:
> Except for this note, I do not get any other warning when I generate the
> .tpr files. The cut-of
Original Message -
>> From: Sai Pooja
>> Date: Monday, November 1, 2010 8:12
>> Subject: Re: [gmx-users] LINCS vs SHAKE
>> To: Discussion list for GROMACS users
>>
>> Yes, I understand that. But then this is a protein in water simulation
>>> with CHarm
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users
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
- Original Message -
From: Sai Pooja
Date: Monday, November 1, 2010 8:12
Subject: Re: [gmx-users] LINCS vs SHAKE
To: Discussion list for GROMACS users
> Yes, I understand that. But then this is a protein in water simulation with
> CHarmm forcefield and I cannot find a reason
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 H
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
si
Mark, I am quite sure that a difference in the overall simulation time
between two replicas is not going to introduce any bias. Still, you
bring up a good point. If the energy distribution (or even worse, its
average) at a given temperature is affected by the timestep, then this
would be a
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 (
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 time
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