Could anyone please explain the difference between how umbrella and
constaint options in the pulling code work. Based on the manual, I
expect that the only difference
is that umbrella used harmonic potential to bind pulled group to the
reference group (point), while constraint uses shake algorithm
I might be wrong here, but my expectation is that nowadays you should
not do anything explicitly in this regard. The compensating charge is
automatically applied.
Dr. Vitaly V. Chaban
On Sat, Nov 30, 2013 at 5:14 PM, Benrezkallah Djamila
benrezkal...@gmail.com wrote:
Dear gmx_users,
My
The output you got indicates that the pulled group came to the
location where it is expected by gromacs to be.
The input looks correct, but gromacs' pull code is with surprise
inside. I would try to pull in opposite direction, i.e. pull_vec1 = -0
0 1. Turning off barostat during pulling also
The fact that images are separated by a distance exceeding the cutoff,
does not mean that they do not interact electrostatically.
I hope the results are not much different...
Dr. Vitaly V. Chaban
On Mon, Dec 2, 2013 at 11:46 PM, Golshan Hejazi
golshan.hej...@yahoo.comwrote:
Hello,
I
The invocation line depends on the MPI tool installed on the cluster.
E.g. in case of openmpi, you write
openmpi -np 64 mdrun -dd 4 4 4
Dr. Vitaly V. Chaban
On Tue, Dec 3, 2013 at 4:58 PM, MUSYOKA THOMMAS
mutemibiochemis...@gmail.com wrote:
Dear Justin,
Well it seems i am the first one to
If the system does not explode, everything is correct. Though your
solution is perhaps in the wrong place in relation to the tube.
Dr. Vitaly V. Chaban
On Tue, Dec 10, 2013 at 10:02 AM, Atila Petrosian
atila.petros...@gmail.com wrote:
Dear Justin
Based on your suggestion, I added C-C bond
I like extreme conditions... Seriously.
OPLS water, as well as other popular MM waters, are parametrized for
liquid state. I think you need to decrease model's dipole moment and
you have to work with an integration time-step to ensure adequate
energy conservation at ca. 600K.
I believe there
On Sat, Feb 15, 2014 at 10:47 PM, CipPruteanu c.prute...@ed.ac.uk wrote:
Dr. Vitaly Chaban wrote
I like extreme conditions... Seriously.
OPLS water, as well as other popular MM waters, are parametrized for
liquid state. I think you need to decrease model's dipole moment and
you have to work
Not sure that I got your question correctly...
The atom indices, which you supply to umbrella code, can be defined as
you like, without being bound to the molecules they belong to in the
topology files. Therefore, if you need to restraint certain number of
atoms in a system, just enumerate them
I am under impression that pulling code performs this trick.
Dr. Vitaly V. Chaban
On Mon, Feb 17, 2014 at 2:27 PM, Steven Neumann s.neuman...@gmail.com wrote:
Dear Gmx Users,
Do you know whether it is possible to apply bonds/distance restraints or
constraints between two atom belonging to
it has nothing to do with CG description of PES.
try the option of trjconv, which is to make molecules whole again
Dr. Vitaly V. Chaban
On Sat, Feb 22, 2014 at 6:43 PM, Nikhil Agrawal nikhil.08...@gmail.com wrote:
Hi All,
I have simulated a membrane proteins system using coarse grain model.
I do not know what the manual says, but if you are talking about
viscosity computation through cos-like acceleration, then g_energy is
doing all the work for you.
Dr. Vitaly V. Chaban
On Fri, Feb 21, 2014 at 10:38 PM, Marcelo Vanean vanea...@gmail.com wrote:
I am trying to calculate the
step-by-step
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 9:51 AM, maryam haji maryam6...@gmail.com wrote:
Dear all
My system consists of protein and CNT. I know I can calculate
Interaction energy and interface area using g_energy and g_sas tools,
respectively.
I want to obtain
are you sure that your binary is parallel?
how many frames do those trajectory files contain?
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 5:32 PM, Marcelo Depólo marcelodep...@gmail.com wrote:
Maybe I should explain it better.
I am using *mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o
I believe you are now posing the questions, where you are expected to
open the source code yourself and read...
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 8:25 PM, Marcelo Vanean vanea...@gmail.com wrote:
Still about the question of temperature coupling with method of the
periodic
sorry, and what performance did you expect from REMD?
Dr. Vitaly V. Chaban
On Mon, Feb 24, 2014 at 8:32 AM, Singam Karthick sikar...@yahoo.in wrote:
Dear members,
I am trying to run REMD simulation for poly Alanine (12 residue) system. I
used remd generator to get the range of temperature
your average pressure is the pressure you should report in the
publication. if you got 5 bars instead of 1 bar, you should write
I simulated the system at 5 bars
Dr. Vitaly V. Chaban
On Tue, Feb 25, 2014 at 6:01 AM, sujithkakkat . sujithk...@gmail.com wrote:
On Mon, Feb 24, 2014 at 5:37 AM,
.
Dr. Vitaly V. Chaban
On Tue, Feb 25, 2014 at 6:48 AM, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
in that case the average is reasonable, but you should state in the
manuscript that all the reported results correspond to 5.15 bar.
Dr. Vitaly V. Chaban
On Tue, Feb 25, 2014 at 10:42
I have looked up tabulated potential in the manual and also the suggested
document, neither of them actually helps the situation.
Why do they not?
Dr. Vitaly V. Chaban
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if the system sends a termination request to MDRUN, it stops the main
cycle and writes down the summary of the run.
Dr. Vitaly V. Chaban
On Wed, Feb 26, 2014 at 10:31 AM, delara aghaie d_agh...@yahoo.com wrote:
Dear Gromacs users,
we want to simulateHSA protein using8 processors. Usually
editconf -box X Y Z
Dr. Vitaly V. Chaban
On Wed, Feb 26, 2014 at 7:58 PM, decaiyu d...@dow.com wrote:
Dear All,
I ran a NVT simulation with a layer of oil+vaccuum.
Because of periodic boundary condition, there are some molecules on the top
of vaccuum layer.
Now I want to increase the
of files that you request.
2014-02-23 22:21 GMT+01:00 Dr. Vitaly Chaban vvcha...@gmail.com:
You do not provide all the details. As was pointed at the very
beginning, most likely you have incorrect parallelism in this case.
Can you post all the files you obtain for people to inspect?
Dr. Vitaly
I have executed for two times, each time i get different error.
And you got *different* errors... What's the difference?
Did you get the error at exactly the same integration time-step?
Did you try to resproduce the error on another disk partition?
Dr. Vitaly V. Chaban
--
Gromacs Users
Hi Valentina -
Honestly, I did not get the considerations with charges. TI probably
scales interaction energies between selected groups, not charges.
Science-wise, I would first decouple organic particle, then decouple
chloride anions, and place a right sign between these two free
energies. If
Since I do not couple intramolecular interactions, why those dihedrals
play any role?
Thank you.
Dr. Vitaly V. Chaban
On Mon, Mar 31, 2014 at 5:33 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Program mdrun_mpi, VERSION 4.6.2
Source code file:
/gromacs-2014.01.14-12-21-22-nbreLi.itsi
Program mdrun_mpi, VERSION 4.6.2
Source code file:
/gromacs-2014.01.14-12-21-22-nbreLi.itsi/gromacs-4.6.2/src/gmxlib/topsort.c,
line: 136
Fatal error:
Function type Fourier Dih. not implemented in ip_pert
What is this while running free energy code? How to get rid og it?
free-energy = yes
The positive values must be expected only if the drugs are ionized...
Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 6:23 PM, Manuel Azenha maze...@fc.up.pt wrote:
Dear all,
When I simulate a solution of a drug in water/methanol to study the
self-aggregation, and try to determine the
then that is rubbish. But, if that is gonna translate into 100%
improvement (halve the production run time), then it is worth upgrading.
That remains to be seen.
Amjad
On Wed, Apr 2, 2014 at 2:44 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
I believe the answer pretty much depends on how large
So, between or intra?
extended intramolecular bonds between cosolvent molecules
Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 8:31 PM, pratibha kapoorpratib...@gmail.com wrote:
Hi all
I have done simulations of my protein in water-cosolvent system (random
initial addition) at 450K. At the end
Hi Everyone -
What is my command line if I need to exclude sites belonging to group
#2 from group #1?
Thank you.
Dr. Vitaly V. Chaban
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seems I achieved that with
1 ! 2
Dr. Vitaly V. Chaban
On Mon, Apr 14, 2014 at 1:52 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Hi Everyone -
What is my command line if I need to exclude sites belonging to group
#2 from group #1?
Thank you.
Dr. Vitaly V. Chaban
--
Gromacs Users
Hi Sukriti Gupta -
Your setup is great. The only scientific problem is that all those
divalent cations in the force fields are being parametrized, to a
larger or a smaller extent, with condensed systems in mind. That is,
if you use them in the liquid phase and for temperature-driven
dynamics, the
First, it is unlikely that 'g_energy -f x.edr -o visc.xvg' provides
you a viscosity.
Second, viscosity from equilibrium MD should converge vs. time before
it can be analyzed. I guess what you observe is viscosity convergence,
not viscosity evolution in response to unfolding.
Dr. Vitaly V.
Nice to know that acidic pH simulations are that easy.
Why do you conclude that you achieved pH 2?
Dr. Vitaly V. Chaban
On Fri, May 9, 2014 at 3:45 PM, Turgay Cakmak turgaycakma...@gmail.com wrote:
Hi all,
I have the 8-residue peptide and I want to do Molecular Dynamics
simulations at pH
This sounds too crazy for me.
Do you have an image of your MD box?
What does 3nm mean for your box? Half of any side?
Dr. Vitaly V. Chaban
On Mon, May 26, 2014 at 8:56 PM, ANDRES ADOLFO ORTEGA GUERRERO
andres.ort...@correounivalle.edu.co wrote:
Hi dear Gromacs User,
I have done a pulling
provided that pulling forces are normally selected (much) larger than
the genuine forces in the simulated system, unfavorable interactions
are unlikely to cause the observed effect. however, rotation is
probably somehow geared by pulling energy. i looked though the movie -
it is like a nice
it is better to avoid rotation at this initial stage. if you
experience certain features in your finals PMFs which you cannot
explain, you will always be unsure where they arrive from. this hurts
your soul.
Dr. Vitaly V. Chaban
On Thu, May 29, 2014 at 9:41 PM, ANDRES ADOLFO ORTEGA GUERRERO
On Jun 5, 2014 8:34 AM, #ZHANG HAIPING# hzhang...@e.ntu.edu.sg wrote:
Dear gromacs user：
I have used follow .mdp to run the replica exchange simulation, after the
simulation, I find the water box become much larger in high temporature
replicas, can anyone tell me how to solve this? By the
no.
Dr. Vitaly V. Chaban
On Mon, Jun 9, 2014 at 3:36 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
Could it possible to run the simulation with reactive force field using
Gromacs?
Nilesh
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There is no rule regarding how many thermostats per system one needs.
Often people choose separate thermostats for parts of system, which
exhibit different mobility. I do not see any connection to functional
forms of the interactions and, therefore, to force fields.
Dr. Vitaly V. Chaban
On
Of course, no. You need to adjust your topology (force field?) to
distinguish between cis- and trans- states.
Dr. Vitaly V. Chaban
On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy venkat...@gmail.com wrote:
Dear all,
I want to simulate a membrane protein system. My membrane is composed of
There is no best combination.
The parameters for water for your solute must be derived using
physically equivalent procedures.
That's all.
Dr. Vitaly V. Chaban
On Thu, Jun 19, 2014 at 11:59 AM, Mohsen Ramezanpour
ramezanpour.moh...@gmail.com wrote:
Dear Gromacs Users,
I have read some
Can you perhaps kindly explain us how charges and non-bonded
interaction values were experimentally determined?
Dr. Vitaly V. Chaban
On Tue, Jun 24, 2014 at 10:37 AM, Rj ra...@kaist.ac.kr wrote:
Dear all,
Experimentally determined charges and non-bonded interaction values for
ligand atoms
you for your concern.
Msg: 3
Date: Tue, 24 Jun 2014 11:26:02 +0200
From: Dr. Vitaly Chaban vvcha...@gmail.com
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Charges non-bonded interaction values usage
in different force fields
Message-ID:
capxdd+y4fndzeel-d+wect_tmfjkq0co28dmhbsgcxgdrvc
It is very easy. You apply an electric field and observe how DL is forming.
Have fun.
Dr. Vitaly V. Chaban
On Fri, Jun 27, 2014 at 3:14 PM, Andy Chao ac...@energiaq.com wrote:
Dear Users,
Would you please suggest a few examples of using GROMACS to simulate an
EDLC device?
Thanks a lot!
Simulation of doped nanostructures is much more complicated than
described below. You must account for the effect of your new fragments
on electron density of the entire nanostructure. There is enough
evidence that an additive approach fails here.
Good luck.
Dr. Vitaly V. Chaban
On Mon, Jun
You need to set the box vectors with respect to system density or
anticipated system density.
Dr. Vitaly V. Chaban
On Sun, Jun 29, 2014 at 9:06 PM, Todor Antonijevic t_ant...@uncg.edu wrote:
Hi,
I cannot obtain the last line (box vectors *1.82060 1.82060 1.82060*) of
the .gro file.
*Can
I believe x2top works nice only when you have a single molecule in a
structure file.
Perhaps, the algorithm wants to connect molecules, which are not
actually connected, and goes crazy, but it is just a guess.
Dr. Vitaly V. Chaban
On Mon, Jun 30, 2014 at 5:46 AM, Andy Chao ac...@energiaq.com
the statement,
You must account for the effect of your new fragments on electron density
of the entire nanostructure.
a little bit further.
thanks for your time
On Mon, Jun 30, 2014 at 4:01 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
Simulation of doped nanostructures is much more
reply. So, the changes like dihedral
angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
there any other adjustments I should make to build the trans lipid isomer
topology from cis? Thank you for your valuable time and concern.
On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly
Graphene topology is like for tube, so
C C
C ... C ... C
C C C C
to the N2T file and you are done.
Dr. Vitaly V. Chaban
On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
Dear all,
I want to simulate
unless your pc is kidding you, there is a problem with index group assignment.
Dr. Vitaly V. Chaban
On Sat, Jul 19, 2014 at 3:56 AM, ANDRES ADOLFO ORTEGA GUERRERO
andres.ort...@correounivalle.edu.co wrote:
Hi dear Gromacs users, i would like to report something maybe could be a
bug or a
1) g_energy -vis is always Einstein
g_energy and then select 1/visc term - NE method.
2) I do not think it makes physical sense to distinguish between
viscosities in a mixture because of the definition of viscosity.
Specifying cos-acc will supply extra energy to all particles.
3) Rigorously,
Use g_angle and your index file must contain triples of the involved atoms.
if I remember correctly, this route provides a gaussian-type
probability distribution, i.e. not evolution vs. time.
Dr. Vitaly V. Chaban
On Wed, Jul 23, 2014 at 9:53 AM, Cyrus Djahedi cyrus...@kth.se wrote:
Hi!
Im
Ionic and atomic radii are the same..? Wow!
You should reparametrize Fe(+++) obviously.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Fri, Jul 25, 2014 at 1:39 PM, #SUKRITI GUPTA#
sukriti...@e.ntu.edu.sg wrote:
Dear Gromacs users,
I wanted to simulate metal ions in gromacs. For Fe+2, I
There is no command, but your can obviously compute formation energy
of your structure.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Jul 28, 2014 at 6:05 PM, Andy Chao ac...@energiaq.com wrote:
Dear gromacs users:
is there any gromacs command that can allow us to compute the
Unless you symmetrize the PMF before output, it should be along an
entire box side.
You do not specify how you pulled your molecule; therefore, it is
impossible to suggest further.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Tue, Jul 29, 2014 at 1:42 AM, Yoo Chan Myung
On Tue, Sep 2, 2014 at 10:59 AM, soumadwip ghosh
soumadwipgh...@gmail.com wrote:
Hello,
I am a newbie to MD simulation. We are working in the direction of
finding the molecular origin of internal friction of protein folding. For
this we have to run folding simulations at different
Why not? Your interaction potential is responsible for everything.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Sep 15, 2014 at 7:27 PM, Александр Селютин saga1...@gmail.com wrote:
Can the gromacs simulate the growth of the molecule?
For example, does it allow to add units to the
Indeed, it is unlikely that averaged coordinates of certain structure
versus time correspond to something physically meaningful.
How do you average them, by the way? And what for, please?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Tue, Sep 30, 2014 at 12:47 PM, Justin Lemkul
And one trivial coin from me...
Not only the random seed for the initial velocity distribution must be
altered, but it is also very good to start from a significantly
different set of coordinates.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sat, Oct 4, 2014 at 11:15 PM, fatemeh ramezani
what is it needed for?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu johnny.lu...@gmail.com wrote:
Hi.
Is it a good idea to mimic NVE by a NVT simulation with a large temperature
coupling time constant, to reduce the effect of the thermostat ?
, Antonio Baptista bapti...@itqb.unl.pt wrote:
Then, run true NVE, for the reasons we already pointed.
On Sat, 11 Oct 2014, Johnny Lu wrote:
For dynamics with correct rate and correct fluctuation.
On Sat, Oct 11, 2014 at 8:09 AM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
what is it needed
seems insignificant over 100 ns
simulation by linear regression fitting on a 300 ps run.
But double precision gromacs can't use gpu and is much slower than single
precision gromacs.
On Sat, Oct 11, 2014 at 4:33 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
I also cannot get why not to just
What about taking another alkali ion (are thery any in CROMOS53?) and
adjusting sigmaepsilon to reflect smaller size of Li(+)?
Of course, lithium is a pretty polarizable guy with certain covalent
bonding ambitions, but this does not prevent people to simulate it as
a hard [+1e] sphere...
Dr.
. Two different simulations can
converge, if the string of random numbers used in langevin thermostats is
the same. I'm not sure about V-rescaling.
I agree that all thermostats and barostats likely cause some artifacts in
dynamics.
On Sat, Oct 11, 2014 at 5:29 PM, Dr. Vitaly Chaban vvcha
830 versus 791 kg/m^3 is not that terrible discrepancy in the case of
united-atom models and other details from below...
Acetone falls within the group of those small molecules, which are
easy to (re)parameterize.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sun, Oct 12, 2014 at 11:38
The artifacts are caused by energy leakage. Thermostatting does not
solve them. The problem exists, but you do not see it clearly with
thermostat. For instance, I have an example where a liquid droplet in
vacuum is not stable due to bad energy conservation. Some particles
just sporadically fly
I believe the major problem with energy losses is that your system
never achieves equilibrium.
Thus, all the simulated properties are not what they need to be...
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sun, Oct 12, 2014 at 5:31 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote
The point was that if the energy leaves the system, then the system is
never in equilibrium. Not vice versa, please.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu johnny.lu...@gmail.com wrote:
Why non-equilibrium can cause lost of total energy in
What about trying a larger system, ~10,000 interaction centers?
The performance which you report is much below natural expectations for GROMACS.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Oct 13, 2014 at 10:55 AM, Олег Титов tito...@qsar.chem.msu.ru wrote:
Thanks for you reply.
Yes, it means what you say.
I would decrease the number of bins.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Oct 13, 2014 at 12:47 PM, Johnny Lu johnny.lu...@gmail.com wrote:
Hi. Does that mean the umbrella don't overlap enough at those z ?
Can you make an overlay plot of the
This usually means that your system is not well equilibrated.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 15, 2014 at 6:13 AM, Padmani Sandhu
padmanisandh...@gmail.com wrote:
Hello,
I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded
in POPC lipid
The easiest way is to simulate QM/MM around Fe (+howmuch?).
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 15, 2014 at 7:22 PM, Guangyu Zhu g...@hwi.buffalo.edu wrote:
Hi, I’m a beginner of gromacs. I want to do simulation for a protein with
protein with ferrous or ferric. But
To achieve what you want you need to MANUALLY set the average DENSITY
which you obtained from NPT. That is, you MANUALLY adjust box side
length in the GRO file.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sat, Oct 18, 2014 at 1:47 AM, Johnny Lu johnny.lu...@gmail.com wrote:
I am trying
I believe you are too concentrated on writing questions, so that it
does not leave you time to think about responses.
Try to learn the manual a bit.
Best luck.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sun, Oct 19, 2014 at 4:18 AM, Johnny Lu johnny.lu...@gmail.com wrote:
I searched
].
For a system consisting of graphene, water and (Na+ OH-, or H3O+ Cl-)
ions, if there is nonbonding-parameters specified, will having a different
fudge value (0.5 instead of 1.0) make a difference?
Thank you in advance.
Regards,
Kester
- 원본 메일 -
*보낸사람* : Dr. Vitaly
Yes, it is a typo and not only in this paper.
There is NO plausible explanation why to introduce scaling factors for
the atoms separated by more than 3 bonds.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Oct 20, 2014 at 4:48 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/19/14
Hi -
genbox must work. You add the first molecule, then the second molecule
and so on. So, I suggest to run genbox for a few times and have enough
empty space available in the box. Otherwise, there is a wonderful tool
called PACKMOL.
The acid molecule looks pretty sexy. I guess it will not be
Does anyone happen to remember what the frequencies in
histo-clust.xvg from g_clustsize mean?
Are they directly comparable between different systems?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
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On Wed, Oct 29, 2014 at 6:37 PM, Agnivo Gosai agnivogromac...@gmail.com wrote:
Dear Users
I did a NVT simulation with the following key parameters :-
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = DNA_Protein Water_and_ions
I do not believe it is because of packmol or because of equilibration.
What about trying a different number of cores per job? Sometimes,
certain number of cores do not want to work correctly for certain
systems.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 29, 2014 at 7:07 PM,
The only reason to use semi-isotropic or anisotropic pressure coupling
is your own desire to control pressure components, XX ... ZZ,
differently.
In the case of liquid crystals, I would use semi-isotropic coupling,
but rather perceiving this as a matter of my own taste.
Dr. Vitaly V. Chaban
It is disgusting that the bond dares to stretch... Perhaps, there is
no harmonic bond record for this bond in the topology?
Would you like to provide numbers characterizing this long stretch, perhaps?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 29, 2014 at 11:21 AM, Seera
Honestly, I did not get why fixed alkane molecules should interact
with water in a different manner than normal ones...
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Tue, Oct 28, 2014 at 5:22 PM, RAMON REIGADA SANZ reig...@ub.edu wrote:
Hi Gromacs users,
I want to simulate a
On Thu, Oct 30, 2014 at 5:55 AM, rama david ramadavidgr...@gmail.com wrote:
Dear Friends,
I search the archive to find the answer of my question but I did not get
satisfied answer so I am putting the question in forum.
One of them is as
Sampling over 100 ps is incredibly meaningful...
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Thu, Oct 30, 2014 at 6:49 AM, Agnivo Gosai agnivogromac...@gmail.com wrote:
Dear Users
I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS
4.5.7 single precision.
My
On Thu, Oct 30, 2014 at 12:30 PM, Ioanna Styliari
pax...@nottingham.ac.uk wrote:
Thank you both for your prompt replies.
Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or
is it just by a trial-error approach?
If your number of cores gives an error, try another
the layer of water must be thicker than the interaction cut-off.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Nov 3, 2014 at 8:44 PM, leila salimi leilasal...@gmail.com wrote:
Dear gromacs users,
I want to simulate the conformation of peptide in solution (20 monomers of
, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Tue, Jan 20, 2015 at 8:11 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
What can segmentation fault in g_clustsize indicate?
Usage error, coding error, or insufficient resources. Hard to say which,
on the information you've given
What can segmentation fault in g_clustsize indicate?
The error occurs irrespective of which atom type for clustering we select.
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UPD: all other utilities process this trajectory without problems
generating adequate numerical results.
On Tue, Jan 20, 2015 at 5:11 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
What can segmentation fault in g_clustsize indicate?
The error occurs irrespective of which atom type
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