There are no problems to have ions while using Reaction-Field treatment.
Dr. Vitaly V. Chaban
On Mon, Nov 11, 2013 at 7:06 PM, Justin Lemkul wrote:
>
>
> On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:
>>
>> Hello
>> If I did the MD simulation using PME and neutralized with ions,
MSD is 3D by default.
Dr. Vitaly V. Chaban
On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy wrote:
> Dear all,
> I am simulating a spherical lipid vesicle. I want to calculate the
> diffusion coefficient for each lipid component in 3D. How to calculate it
> using g_msd (or any other tool like g_v
If in vacuum, I would add hydrogens via covalent bonds.
Dr. Vitaly V. Chaban
On Mon, Oct 28, 2013 at 10:29 AM, Richa Singh
wrote:
> Hi all,
>
> I'm trying to run a vacuum simulation of my protein which has a non-zero
> charge.
> How to deal with this charge? Can I add counter ions in to my sys
If the job is not "very parallel", it will not crash.
It is better to preequilibrate in NVT beforehand. Cyclopropylchloride
is probably a liquid at 290K, if the model is parametrized reasonably.
So it should not phase-separate.
Vitaly
On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham wrote:
> On
; between nanotube atom and first atom of my chain or again - LINCS? Both
> chain and nanotube are made of the same type of 8 type of atoms. Please,
> advise.
>
> Steven
>
>
> On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban
> wrote:
>>
>> I am just
Unlikely possible... But yeah, the feature might be handy.
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 4:20 PM, grita wrote:
> Hi guys,
>
> Is it possible to specify in the topol.top file preprocessor statements, so
> that you can stop the simulation prematurely?
>
> I pull two molecules toge
I am just curious why the system would explode without
"periodic_molecules = yes". If the PBC procedure is applied before
harmonic bond potential is calculated, than the opposite nanotube
atoms should be (already) seen as neighboring. This looks the same as
the solvent molecule, one atom of which c
I do not think that I ever tried myself, but is seems all the same.
Why do you ask?
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy wrote:
> Dear all,
> I have a basic doubt. Is there any difference between the two processes
> where
> 1) I concatenate the trajectories and do
I think this is in topology, not in MDP. With PBC, you just specify
what happens to the particle after it crosses the edge of the box in
certain direction.
I have no preference regarding LINCS vs harmonic bonds.
You can also "freeze" only the rim atoms of the nanotube from both
ends and this will
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 2:10 PM, Justin Lemkul wrote:
>
>
> On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote:
>>
>> Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
>> get the following error:
>>
>> Select a group: 0
&
On Mon, Sep 23, 2013 at 2:40 PM, Jong Wha Lee wrote:
> Dear Vitaly,
>
>
>
> Thank you for your suggestion.
>
>
>
> I have also tried calculating interaction energies by specifying energygrps
> in .mdp file, but calculated energies deviate greatly from QM calculated
> energies and experimental resu
Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
get the following error:
Select a group: 0
Selected 0: 'System'
Reading frame 0 time0.000
Precision of traj.xtc is 0.004 (nm)
Using output precision of 0.001 (nm)
Back Off! I just backed up confout.gro to ./#confout.gr
I am confused. Why do you want 4-sites water?
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 10:36 AM, ABEL Stephane 175950
wrote:
> Hello all,
>
> It is not a gromacs problem "per se", but I hope that some gromacs users can
> help me. I would to do simulations of phospholipid bilayers with the
Dear Jonathan -
Is it not a PBC effect? Try to display atoms as spheres - it will look
better. Otherwise, use the options in trjconv to remove PBC in the
visualized structure(s).
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 9:22 AM, Jonathan Saboury wrote:
> I tried minimizing a box of cyclohe
Dear John -
I think you can achieve the goal even faster if you just define two
groups, such as MOL1 and MOL2 in MDP and then see the interaction
energy between them using g_energy.
5% is a decent agreement. Usually, even basis set superposition error
is larger (if you include this correction).
the smart way is to constrain everything at once in MDP...
Dr. Vitaly V. Chaban
On Tue, Sep 17, 2013 at 10:50 PM, HANNIBAL LECTER
wrote:
> Is there a smart way of writing the constraint sections in the topology
> file other than entering the values manually ?
>
>
> On Tue, Sep 17, 2013 at 10:10
s by specifying it
> in the atomname2type.n2t file. I am still not sure as to what is the source
> of this discrepancy. After a few tests I think this can be caused by
> improper parameterization of the bonds but I am not sure how to go about
> correcting any discrepancies.
>
>
> On Fri,
I would guess that the density is zero at the center, since you do not have
solvent molecules inside the membrane.
Yes, the output density is number of interaction sites per nm^3, calculated
in each slice, whose size you had specified.
Dr. Vitaly V. Chaban
On Sun, Sep 15, 2013 at 5:23 PM, Sun
The [numerical] results will depend on architecture you are running on. No
matter where the binary input file was prepared.
Dr. Vitaly V. Chaban
On Sun, Sep 15, 2013 at 10:22 AM, Albert wrote:
> Hello:
>
> I've got a md.tpr file generated by grompp, I am just wondering will the
> results be
g_mindist also has something useful in this direction, I guess.
Dr. Vitaly V. Chaban
On Sat, Sep 14, 2013 at 12:10 AM, Rama wrote:
>
> Hi ,
>
> I there any tool to calculate distance between particular atom from one
> group(protein) to particular atom from another group(DMPC lipid in
> Bilay
rameters for CNT.
>
>
> On Fri, Sep 13, 2013 at 1:50 PM, HANNIBAL LECTER <
> hanniballecte...@gmail.com> wrote:
>
>> I am position restraining the CNT group. That affects the degrees of
>> freedom.
>> On Sep 13, 2013 1:43 PM, "Dr. Vitaly Chaban" wro
There must be some problem with degrees of freedom in your system...
Dr. Vitaly V. Chaban
-- Forwarded message --
From: HANNIBAL LECTER
Date: Fri, Sep 13, 2013 at 7:15 PM
Subject: [gmx-users] SD integrator
To: Discussion list for GROMACS users
Hi all,
I have been posting fo
k and see the role of GaussView in GROMACS.
> Thank you.
> http://www.hindawi.com/journals/chem/2013/803151/
>
>
> On Mon, Sep 9, 2013 at 12:46 PM, Dr. Vitaly Chaban wrote:
>
>> Hmmm
>>
>> GaussView is a supplement to Gaussian to prepare input files and visual
Hmmm
GaussView is a supplement to Gaussian to prepare input files and visualize
some (but far not all) results. Of course, it has nothing to do with
gromacs and its topologies.
Or, do I misunderstand you?
Dr. Vitaly V. Chaban
On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS <
mutemibiochem
I think it is a dangerous practice to simulate with a cutoff of 0.5 nm.
Irrespectively of what you study.
Dr. Vitaly V. Chaban
On Fri, Aug 30, 2013 at 11:32 AM, Valentina wrote:
> Thank you for your reply.
>
> My box is quite small indeed, so my cut-offs are 0.5
>
> If I make a single layer, I
No, it is not. But you can at least convert coordinates via VMD.
If you want to use gromacs trajectory analysis tools, it is easier to
convert NAMD trajectory to gromacs trajectory. Otherwise, I have no idea
why one may need to jump between codes.
Dr. Vitaly V. Chaban
On Fri, Aug 16, 2013 at 10
I like CHARMM.
Dr. Vitaly V. Chaban
On Mon, Aug 12, 2013 at 2:19 PM, Maria Astón Serrano <
m.aston.serr...@gmail.com> wrote:
> Dear Gromacs users,
>
> We would like to know which is the Force Field which is customarily
> preferred for simulations of peptides and proteins.
>
> Thank you very muc
Via an index file, I would guess... Or what do you mean exactly?
Dr. Vitaly V. Chaban
On Mon, Aug 12, 2013 at 5:26 AM, Kieu Thu Nguyen wrote:
> Dear users,
>
> I want to use g_msd to measure diffusion coefficients of lipid bilayer. But
> i do not know how to choose the reference atom per lipid
Soneone said here that static versions are impossible for Cray...
Dr. Vitaly V. Chaban
On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner wrote:
> Hi
>
> I am having problems creating static versions of the GROMACS binaries for
> a Cray XE6 (www.hector.ac.uk). The build process I am using is d
I am afraid you will need to derive it from scratch.
There should be some studies about perchlorate salts in literature. Make a
search.
Dr. Vitaly V. Chaban
On Tue, Jul 16, 2013 at 6:08 AM, Sushma Yadav wrote:
> Dear users,
>
> How do I get the force-field for ClO4- ion in the gromacs?
>
>
H = U +pV, all these terms are available through g_energy.
Your resulting values will be per mole, so I would perform no additional
normalization.
Personally, I would simulate all cases (folded, unfolded, etc) with the
same number of waters -- to avoid any possible artifacts.
Dr. Vitaly V. Cha
Sure, you can.
Dr. Vitaly V. Chaban
On Mon, Jul 15, 2013 at 8:38 AM, wrote:
> Hi
>
> I want calculate the enthalpy of water molecule corresponding to protein
> folded and unfolded state.
> How much a single water molecule (enthalpy and free energy) contribute in
> folding ?
> Can we calculat
look for either "-dt" or "-skip".
Dr. Vitaly V. Chaban
On Mon, Jul 15, 2013 at 2:03 AM, Rama wrote:
> Hi,
>
> How to get a snapshots in equal intervals of time (250ps) from production
> MD
> trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
> file.
>
>
>
> --
> View
On Thu, Jul 11, 2013 at 1:17 PM, Steven Neumann wrote:
> Thank you. Another question: Does RDF depends on the mass of the atom? On
> the one hand it gives different value of the force in equation of motion
> but on the other hand velocities are rescaled with a thermostat.
>
>
It does not. Provide
if you prepare a separate ITP for each solvent, you will save some nerves
in the long term
Dr. Vitaly V. Chaban
On Thu, Jul 11, 2013 at 7:14 PM, Justin Lemkul wrote:
>
>
> On 7/11/13 8:59 AM, Shima Arasteh wrote:
>
>> Dear all,
>>
>> I see cyclohexane parameters in top & par CGenFF files
> ya.. but there is experimental data to confirm the presence. can you help
> me to solve this problem
>
>
> On 9 July 2013 11:54, Dr. Vitaly Chaban wrote:
>
>> Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will
>> obviously not sit in
?... do I need to simply add the xe parameters to .gro
> file and topol file? or may i need to make changes in forcefield? pls help
>
> Thanking you
> Divya
>
>
> On 8 July 2013 19:16, Dr. Vitaly Chaban wrote:
>
>> I am a too curious person not to ask WHY Xe is of
I am a too curious person not to ask WHY Xe is of interest in connection
with the protein..?
Dr. Vitaly V. Chaban
On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul wrote:
>
>
> On 7/8/13 9:21 AM, divyasunil wrote:
>
>> Hello,
>>
>> Please help me to add Xe atom to GROMOS96 53a6 force field. I nee
I think this question is for the developers of your operating system ...
Dr. Vitaly V. Chaban
On Sat, Jul 6, 2013 at 6:10 PM, Hari Pandey wrote:
> Hi all gromacs users,
> I have new forcefield and I have this folder in my working directory as
> well as in /share/gromacs/top. When I run pdb
l have to run shell MD in NAMD, though it will be slower a bit.
> Seemingly, only Vitaly see my problem :).
>
>
> 05.07.2013, 16:31, "Dr. Vitaly Chaban" :
> > The was a bug report on this error a few years ago,
> > http://redmine.gromacs.org/issues/332
>
5.07.2013, 14:48, "Dr. Vitaly Chaban" :
> > In which case can the determinant not be computed?
> >
> > Dr. Vitaly V. Chaban
> >
> > On Thu, Jul 4, 2013 at 10:53 AM, Sergey wrote:
> >
> >> Dear users,
> >>
> >> I'm t
In which case can the determinant not be computed?
Dr. Vitaly V. Chaban
On Thu, Jul 4, 2013 at 10:53 AM, Sergey wrote:
> Dear users,
>
> I'm trying to run MD with SWM4-DP model (data from
> http://virtualchemistry.org), but I always have error:
> "Can not invert matrix, determinant =".
>
> I
"g_integrate" should be "g_analyze" below. Sorry.
On Fri, Jul 5, 2013 at 12:20 PM, Dr. Vitaly Chaban wrote:
> Use this command line:
>
> -- g_velacc -nonormalize -acflen 2001
> -- g_integrate -f vac.xvg -integrate
> -- Multiply the resulting value by
Use this command line:
-- g_velacc -nonormalize -acflen 2001
-- g_integrate -f vac.xvg -integrate
-- Multiply the resulting value by 333.333, the result will be
self-diffusion coefficient expressed as result * 10^(-9) m^2/s.
The velocities should be written down at least every 10fs during MD. The
It would be nice to see plotted velocity autocorrelation function, VACF,
which you integrate?
The resulting diffusion constant looks crazy large, so there must be
something rotten in the VACF.
Dr. Vitaly V. Chaban
On Thu, Jul 4, 2013 at 8:32 AM, Ishwor wrote:
> I have really tried to calcul
why not to pick up a QM technique to study the "interaction"?
Dr. Vitaly V. Chaban
On Thu, Jul 4, 2013 at 3:58 AM, Jong Wha Lee wrote:
> Thank you Mark and Vitaly.
>
>
>
> I understand that simulation of protons in the solution phase is
> unphysical.
> Though I haven't mentioned beforehand, I'm
I would guess the new atom type should be in the ITP file. And of course,
you are expected to define bonded and nonbonded terms for all applicable
pairs, triples... of atoms.
Good luck.
Dr. Vitaly V. Chaban
On Wed, Jul 3, 2013 at 6:41 PM, Juganta K. Roy wrote:
> Dear all,
>
> I am a new user
I am also not aware of the force field parameters for hydrated/solvated
proton, but maybe I am just wrong here.
An attempt to describe proton with Newtonian dynamics will unlikely give
you anything similar to reality. Lennard-Jones parameters play no role
here, by the way, some force fields assign
Hi Oliver -
Hmm. Did you try to start from (a little bit) different configurations
on the problematic machine? Or re-install gromacs there, perhaps?
Dr. Vitaly Chaban
On Thu, Jun 20, 2013 at 3:44 PM, Oliver Schillinger
wrote:
> Dear Gromacs users,
>
> I experience a ver
According to your MD parameters, your system should attain T=300K at the 300th
nanosecond.
Since you have run only for 50 * 0.002 ps = 1ns, you got T=1K, since
temperature elevates linearly, based on your setup.
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 8:07 PM, Marc Hömberger wrote
what happens to your energy before the observed crash? does the crash
happen at the same time-step each time?
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 5:22 PM, Neha wrote:
> Hi everybody,
>
> I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman
> coupling
Steven -
I probably know nothing about "function #2", but "function 1" is used just
everywhere. It does constrain intramolecular distances.
Good luck. Vitaly
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 4:46 PM, Steven Neumann wrote:
> I was not sure about the fucntion
On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul wrote:
>
>
> On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:
>
>> This problem indeed happens from time to time. With versions 4.5+ it is
>> more frequent than with versions up to 4.0.7. It is not always connected
>> to
th the number of temperature coupling groups. You have
defined less than you expect, as the program requests only 9 values. So,
refer to the number of points to T annealing, which you do not list here.
Dr. Vitaly Chaban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org
larger *spatially) system you simulate, the more likely it to appear.
The simple advice is to reduce the time-step, but it is not to be
understood as a universal treatment.
Of course, you can reinitialize your charge groups, as this is better
connected with the below error message.
Dr. Vitaly
I think all is correct.
Why are you asking? People normally report problems.
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I am running CG simulation and I wish my beads to be constraint - one away
> from each other of 0.4 nm.
It is *desirable*.
In many cases of free energy calculations, single precision is still
reliable.
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 7:35 AM, Albert wrote:
> Hello :
>
> I am going to use Gromacs with PLUMD plugin to perform Metadynamics.
> Since this methods invo
I do not know about the newest versions, but in older ones ngmx was missed
when you did not have the lesstif library installed.
Dr. Vitaly Chaban
On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury wrote:
> Dear gmx users,
>
> I had installed gromacs 4.6.1 using cmake. All the
Nohow.
Numbers in GRO files serve exclusively decorative function.
Dr. Vitaly Chaban
On Tue, Jun 4, 2013 at 4:12 PM, Bao Kai wrote:
> Hi,
>
>
> I guess the renumbering of the atoms and molecules will be a problem,
> especially when the two boxes contain the same type o
editconf is a nice tool to create vacuum in your box. You can then insert
one of your box into another box using cat box1.gro box2.gro, just remove
the very last line in box1.gro.
Dr. Vitaly Chaban
On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai wrote:
> Hi, all,
>
> I want
Can g_angle not handle this?
Dr. Vitaly Chaban
On Sat, Jun 1, 2013 at 10:15 AM, larif sofiene wrote:
> Greeting
> I'm trying to find the angle between a cation and a benzene cycle from a MD
> trajectory. I'm really confused is there a tool for such calculations ?
&g
Hmmm...
And what does the observed difference look like, numerically?
On Thu, May 30, 2013 at 10:14 AM, Mark Abraham wrote:
> No charges = no problem. You can trivially test this yourself with mdrun
> -rerun ;-) Manual 4.1.4 talks about what RF is doing.
>
> Mark
>
>
> On Thu, May 30, 2013
In GRO file, the atom numbers do not really matter. Just use any number you
like. It will work correctly.
mdrun will renumber atoms from 9, as it likes, automatically.
Dr. Vitaly Chaban
On Thu, May 30, 2013 at 4:57 AM, Phil wrote:
> I'm working on a .GRO file and have come
perhaps mdrun -cpi -deffnm full
will also do the job in your case
On Wed, May 29, 2013 at 6:36 PM, Dr. Vitaly Chaban wrote:
> I do not remember all the keys.
>
> Rename your files to their default names and you will have nothing to
> specify except
>
> mdrun -cpi
>
&
I do not remember all the keys.
Rename your files to their default names and you will have nothing to
specify except
mdrun -cpi
On Wed, May 29, 2013 at 6:31 PM, Fábio Filippi Matioli <
fabiof...@hotmail.com> wrote:
> Hello, i'm who asked about extending simulations.
> You sad for me pen teh
The force should not probably exceed kT product too much...
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 3:19 PM, Sathish Kumar wrote:
> Dear Sir,
> In pulling simulations how to set pull_rate and
> pull_k .On which basis we can set these values.
>
pending requested, but only 2 of the 4 output files are present
>
> Tnks
>
>
>
I believe the idea is that you should have trajectory file, energy file,
logfile, etc, so that gromacs could append them. If they have non-default
name, you probably should specify them explicitly in the invoc
. Why don't you want to use molecular dynamics?
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 4:10 PM, Mohan maruthi sena
wrote:
> Hello Sir ,
> Thanks for your quick reply. I have used bd_fric =0 and then my
> simulation is blowing up. I have used a time step of 0.002ps, Hence
According to my understanding, setting friction coefficient is quite a
personal thing. The higher is bd-fric, the smaller are velocities.
Why not to set bd-fric = 0 in order to start with? See manual for details
of how this trick works.
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 11:48 AM
If you want to observe H-bond dynamics and do it with an atomistic
precision than, of course, you need an all-atom representation. United
atoms will still *effectively* account for H-bonding, if you are happy with
reduced precision.
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 8:01 AM, Revthi
Aside from original question, you will probably want to initialize
velocities (gen_vel) in order to evolve a different trajectory rather than
repeating previous one.
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 1:00 PM, Dr. Vitaly Chaban wrote:
> If the frame was saved to the trajectory f
If the frame was saved to the trajectory file, just extract it with
trjconv -dump $timeframe -o conf.gro
and continue your MD.
No need for any additional energy minimizations, of course.
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 12:45 PM, Андрей Гончар wrote:
> Hello, I'
without knowing full details of your simulated system and the goals you
pose, I cannot advise anything more definite than I did before.
if I were you and my system were yours, I would start with MARTINI FF.
I wish you a success in your endeavor.
Dr. Vitaly Chaban
On Tue, May 28, 2013 at 6
In my mind, MARTINI is a decent option to build your particular topology
upon.
Dr. Vitaly Chaban
On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker wrote:
> Dear all,
> I am a beginner to performing simulations and my system consists of
> protein+ cholesteryl ester +phospholipid and dru
Look for my papers. At least, two dozens of them are about non-biophysical
stuff.
Gromacs can. The question is whether you can provide an adequate
Hamiltonian to describe your systems involving Al-surface.
Dr. Vitaly Chaban
On Mon, May 27, 2013 at 10:59 PM, Jeya vimalan wrote:
> D
if there are many values in the literature, what do you want?
On Mon, May 27, 2013 at 4:29 PM, Ishwor Poudyal wrote:
> Dear all.I want to study simulation of carbonmonoxide in water...I get
> different values of force constant partial charge while searching for those
> constants. Can anyone hel
Of course, you can simulate what you like, but I would personally use an
all-atom representation for long hydrocarbons. I think explicit hydrogens
matter for conformations.
V.V. Chaban
On Thu, May 23, 2013 at 5:16 PM, Bao Kai wrote:
> Hi, all,
>
> I finally wrote a decane topology file. I u
UPD: the version of gromacs exhibiting this marvellous behavior is 4.5.5.
On Mon, May 20, 2013 at 8:11 AM, Dr. Vitaly Chaban wrote:
> any ideas what the below error message can indicate?
>
> Step 350755:
> The charge group starting at atom 44257 moved than the distance allowed by
that it happens?
Thank you. Dr. Vitaly Chaban
--
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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electrostatic
charges for each site.
Dr. Vitaly Chaban
On Thu, May 9, 2013 at 11:33 PM, Eric Stokes wrote:
> Hello,
>
> I am attempting to generate force-field parameters for a fatty acid
> molecule that contains a carboxilic acid head group. I decided to use the
> parameters for
Your problem has nothing to do with barostat.
There is such thing as DispCorr. I am unsure whether if should be turned on
or off in case of your model. It does influence density to certain extent.
Dr. Vitaly Chaban
> -Original Message-
> From: gmx-users-boun...@groma
I think you can process the trajectories without generating TPR.
Dr. Vitaly Chaban
On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy wrote:
> Dear gromacs users,
>
> I am analyzing trajectories of an ionic liquid system generated using AMBER
> MD package. The force field parameters ar
LINCS doesn't like your system... or your system doesn't like LINCS...
You can decrease the time-step as the simplest action.
Dr. Vitaly Chaban
On Thu, May 2, 2013 at 2:40 PM, Souilem Safa wrote:
> Dear Gromacs users ,
> I did the simulation of a single molecule
;
>
>
1) When packing parameter of the the lipid is large enough.
&
2) When concentration of lipids in the box is reasonably low.
Dr. Vitaly Chaban
> thank you very much
> Albert
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/*
The resulting MSD will correspond to the average from individual atoms.
Calculating MSD of an individual atom and ascribing it to a [small]
molecule, which this atom belongs to, is reasonable. Assuming that averaged
MSD from atoms correspond to the cluster they form is not.
Dr. Vitaly Chaban
t;
> Aren't the keywords here "charged system" + "PME"?
>
>
> Dr. Vitaly Chaban
>
>
>
> On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole wrote:
>
> >
> > Did you visualise the system? T in function of time? Epot in function of
> >
The salvation is to use:
mdrun -cpi state.cpt
Dr. Vitaly Chaban
On Thu, Apr 25, 2013 at 2:37 PM, Justin Lemkul wrote:
>
>
>> Can any body tell me how do it split script i such that i will get all
>> 20ns simulation
>>
>>
> You specified a given ti
Hmmm
Aren't the keywords here "charged system" + "PME"?
Dr. Vitaly Chaban
On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole wrote:
>
> Did you visualise the system? T in function of time? Epot in function of
> time?
>
> As a side note (not relev
"a simple way" is x2top
Dr. Vitaly Chaban
On Mon, Apr 22, 2013 at 1:38 PM, aixintiankong wrote:
> Dear ,
> I want to use charmm force field to simulate the protein and ligand
> system. The protein can selcet charmm27 in gromacs, but i don't konw how to
> get the
avoid any
interactions, which you would not have had in real experiment.
I also expect a specific behavior, if your droplet is very small.
Maybe, I would simulate this system without PBC at all.
Dr. Vitaly Chaban
> I have a graphene like surface (carbons on a hexagonal lattice with z
ethod for viscosity heavily depends on the acceleration
value. Your selection looks reasonable for me, but try to decrease the
value. "Ideal" acceleration depends on the particular collective dynamics
in each system, of course.
I can soothe you ability a workability of the utility. It h
T, after this
> equillibration,
> half of the DPPC along with SOL is no showing in VMD. Could any suggestions
> on this behavior.
>
>
I think your particles are still there...
Try to adjust VMD settings.
Dr. Vitaly Chaban
--
gmx-users mailing listgmx-users@gromacs.org
http:/
On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl wrote:
> Dear Dr. Vitaly Chaban,
>
> Thanks very much again. I am sorry for the unclear, charge transfer was
> also taken into account for the complex, I did not mentioned in the last
> e-mail.
>
> What do you mean by finite T e
On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl wrote:
> Dear Dr. Vitaly Chaban,
>
> Thanks very much for your patient and detailed suggestions on this
> problem. Actually, I am doing what your suggested now.
> I optimized the copper-ligand complex using QM method, and then did some
So there is a problem with your trajectory file. Try to understand what
kind of problem it is.
I can recollect that I experienced something like that why translating CPMD
trajectory to GROMACS. Maybe, it does not write time for each frame at the
right place -- just a guess.
Dr. Vitaly Chaban
t;
>
> On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban wrote:
>
>> I believe the problem is in the way which you used to convert AMBER
>> trajectory to the GROMACS trajectory
>>
>> I would suggest to try gmxdump and see what your trajectory looks like. Oe
>
On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl wrote:
> Dear Dr. Vitaly Chaban,
>
> Thanks very much for your patient explanation. Yeah, you are right, that
> is what I want to know: how you tuned this parameter?
>
> Since then, if I want to set a new atom type and I know its vd
nteratomic distances AFTER you turn on all
the necessary potentials (Coulombic attraction in case of OPLS).
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 3:14 PM, fantasticqhl wrote:
> Dear Dr. Vitaly Chaban,
>
> Thanks very much for concern on my research! We are going to the use
I believe the problem is in the way which you used to convert AMBER
trajectory to the GROMACS trajectory
I would suggest to try gmxdump and see what your trajectory looks like. Oe
maybe even better - try to visualize it in VMD to see if the format is
correct.
Dr. Vitaly Chaban
Sir
>
?
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl wrote:
> Dear Dr. Vitaly Chaban,
>
> Thanks very much for your explanation. I guess that I get what you mean
> now! Thanks!
>
> All the best,
> Qinghua Liao
>
> On 04/07/2013 11:35 AM, Dr. Vitaly Chaban
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