Dear all,
I'm performing NVT on a system consisting a water layer, a decane layer
and a lipid layer in between those two layers. There are 40 lipids, 627
decane molecules and 8577 water molecules in total.
The EM was conducted successfully, however, when I try to run NVT on
this system, it
Dear Vitaly,
here's the log file of the nvt simulation, and it was killed due to
exceeding the wall time. Hopefully it could still provide some useful
information. Thank you so much indeed!
The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell
Dear All -
I an using the current version of gromacs. Although I have
nstxout = 0
nstvout = 0
nstfout = 0
in the MDP file, the traj.trr file appears during the MD run (and is
quite large). In older versions, there was no traj.trr with such an
On Tue, Sep 18, 2012 at 2:43 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/18/12 8:29 AM, Dr. Vitaly Chaban wrote:
Dear All -
I an using the current version of gromacs. Although I have
nstxout = 0
nstvout = 0
nstfout = 0
in the MDP
. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
Thank you for your comments,
On 10 October 2012 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Thanks..You
By the way, if you place your solvent molecule (-cs .gro) into a
very large box, such as 10x10x10nm, genbox may perform well. I did NOT
try, just an idea.
For the overall system setup, I would rather follow the previous
comments anyway.
On Wed, Oct 10, 2012 at 10:49 PM, Dr. Vitaly Chaban
for the comments,
J.
On 10 October 2012 17:16, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
By the way, if you place your solvent molecule (-cs .gro) into a
very large box, such as 10x10x10nm, genbox may perform well. I did NOT
try, just an idea.
For the overall system setup, I would rather follow
commands that i can check ? Thanks in advance,
On Tue, Oct 23, 2012 at 7:05 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
I have recomplied the -fPIC and its complied well. I have not used mpi
cluster before so have some few doubts on it.
The -fPIC key stands for position independent code
of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
I greatly appreciate your further helps.
Best Wishes
Arman
On Mon, Oct 29, 2012 at 1:20 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
On 10/26/12 3:25 PM, Arman M. Soufiani wrote:
Dear Gromacs users,
I am simulating a protein
If I turn this option on, such as:
pcouple=Isotropic
it is said:
ERROR 1 [file eq.mdp, line 78]:
Pressure coupling not enough values (I need 1)
WARNING 1 [file eq.mdp]:
Turning off pressure coupling for vacuum system
You canNOT use pressure coupling without PBC in gromacs.
:
thanks a lot for kind comments.
Do you have any idea why the running is so slow? Especially considering it
is with GBSA model and my protein is only with 240 aa.
thank you very much
best
Albert
On 11/02/2012 04:30 PM, Dr. Vitaly Chaban wrote:
If I turn this option on, such as:
pcouple
On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo marcelodep...@gmail.com wrote:
I thought that at first, but other softwares run in parallel. If there's a
problem, it' s somehow in the PBS.
My guess is that my PBS don't allow the LAM library see others nodes. But
I have no clue where the
On Wed, Nov 7, 2012 at 11:48 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo marcelodep...@gmail.com
wrote:
I thought that at first, but other softwares run in parallel. If there's a
problem, it' s somehow in the PBS.
My guess is that my PBS
Thank you, Justin. Supplying desired conf.gro is indeed a wise solution.
On Tue, Nov 13, 2012 at 4:02 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/13/12 9:59 AM, Dr. Vitaly Chaban wrote:
Dear All -
Is it possible in the current gromacs to apply position restraints NOT
in respect
Dear Gromacs users,
I tried g_rdf function and have obtained a strange result:
usually the RDF curve looks like relaxing oscillations around 1.0 constant
level,
but in my case it appears to be oscillation around exponent going from 0.0
at zero distance to 1.0 at large distances.
Is the
Hi Juliette N. -
In general -- yes, you are right. Your system probably has tiny point charges...
I would also compare electrostatics terms directly, but they are
unlikely to differ. Or perhaps even better, look at the Coul.-recip.
term. If it small as compared to LJ-(SR) than it is fine to
On Tue, Jan 15, 2013 at 1:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/15/13 7:06 AM, Dr. Vitaly Chaban wrote:
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading
and SSE4.1) I get allways after
On Tue, Jan 15, 2013 at 1:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/15/13 7:06 AM, Dr. Vitaly Chaban wrote:
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading
and SSE4.1) I get allways after
YES.
On Mon, Jan 28, 2013 at 12:51 PM, Shima Arasteh
shima_arasteh2...@yahoo.com wrote:
Am I supposed to skip this step?
Thanks for your reply.
Sincerely,
Shima
___
From: Dr. Vitaly Chaban vvcha...@gmail.com
To: gmx-us...@gromuracs.org
Sent: Monday
Hello
In the g_density manual it is mentioned that
When calculating electron densities, atomnames are used instead of types,
this is bad
So what should be included in the electrons.dat file. The unique atomtypes
of the group or all the atomnames of this group?
Thanks in advance.
I am
of this kind? Is there a way to use this
potential in GROMACS? Do you have any suggestions?
Tabulate it.
Dr. Vitaly Chaban
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there
is no problem in grompp and EM step (except high energy on some atom).
The energy will normalize during molecular dynamics stage.
Dr. Vitaly Chaban
or Do I need to manually remove those overlapping lipids and water
molecules.
Thanks in advance
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(no restarts), or do one run with
g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1
I believe the advice was to increase trestart and you can decide
yourself how much to increase.
Most likely, your protein deserves better sampling than 10 ns for a
linear diffusion.
Dr. Vitaly Chaban
perhaps, you could make a plot??
it is difficult to understand what you are speaking about.
Dr. Vitaly Chaban
On Thu, Mar 28, 2013 at 2:59 PM, Ahmet yıldırım ahmedo...@gmail.com wrote:
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is
there a bug
100 0.1336 0.114
110 0.0899 0.0841
120 0.0572 0.0598
130 0.0506 0.0482
140 0.0723 0.0767
150 0.1466 0.1439
160 0.0703 0.0601
170 0.081 0.0853
180 0.0278 0.027
190 0.1121 0.1024
200 0.3136 0.2981
2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com
if I
- Expected values are estimated. For example 輋 the structure is reach to
converge at last 100 ns ( all simulation time is 200 ns), then in theory,
diffusion coefficients will dont change at last 100 ns.
-I have only one diffusion coefficient for each 10 ns. I have 20 diffusion
coefficients
cell and
run under NVT ?
If you want solvent/air interface, you should add $air.
If you want solvent/vacuum interface, it is enough to extend the box.
If you want liquid/vapor interface, you need to re-equilibrate the system
in NVT with a space for vapor available in the box.
Dr. Vitaly
for this puporse)
I believe surface tension should be calculate ONLY from fixed-volume
simulations. By definition of the property, isn't it?
Thanks!
Dr. Vitaly Chaban
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Dear All -
Does Gromacs possess a convenient utility to [randomly] substitute solvent
particles by given number of multiatomic solutes?
Dr. Vitaly Chaban
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Yes, I can
Could you briefly explain the difference between -cp and -cs options?
On Sun, Mar 31, 2013 at 10:34 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/31/13 4:26 PM, Dr. Vitaly Chaban wrote:
Dear All -
Does Gromacs possess a convenient utility to [randomly] substitute solvent
Hi Elisabeth -
The only explanation is that you actually DID NOT extend the box in Z
direction. Look at the last line of confout.gro.
g_density -d Z gives you a [local] density versus Z coordinate.
Dr. Vitaly Chaban
On Mon, Apr 1, 2013 at 5:33 PM, Elisabeth katesed...@gmail.com wrote:
Hi
I think if you use checkpoint files, the program does not read either MDP,
or GRO, or TOP, or anything except CPT.
Dr. Vitaly Chaban
On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth katesed...@gmail.com wrote:
Hi vitaly,
The initial structure is indeed extended but the final output.gro
It is something very new for me.
If structure, etc are not read from CPT files, why does one need them for...
On Mon, Apr 1, 2013 at 7:21 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
I think if you use checkpoint
Justin -
I am sure mdrun reads coordinates from -cpi state.cpt
Vitaly
On Mon, Apr 1, 2013 at 7:44 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 1, 2013 at 1:29 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
It is something very new for me.
If structure, etc are not read
... or what?
If molecules tend to fill vacuum, it can only mean that the matter you are
simulating is above critical point.
What is your T and what are the particles in your box?
Dr. Vitaly Chaban
I am expecting to see how density changes with Z at the solvent -vacuum
interface
Please
.
And yeah... Forget about NPT and learn the Gibbs phase rule.
Dr. Vitaly Chaban
On 1 April 2013 14:22, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.com wrote:
Hi Vitaly,
The problem was with cpt file since it re sets
There is a wonderful data page devoted to methane in wikipedia...
It follows from this webpage that you will get a perfect density profile if
you decrease your T down to 150K...
On Mon, Apr 1, 2013 at 8:37 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
On Mon, Apr 1, 2013 at 8:29 PM
analysis utilities if the trajectory is
not finished yet (mdrun runs in the same folder and appends the XTC or EDR
file) or if certain frame has not been correctly written down.
Dr. Vitaly Chaban
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and are added to the
other side due to PBC. as a result the density profile does not exactly go
down to zero but tends to zero anyways. I was wondering if this is
considered a liquid-vapor interface?
YES
or it is still liquid-vacuum?
thanks!
On 1 April 2013 14:43, Dr. Vitaly Chaban vvcha
0 to be completely sure.
Dr. Vitaly Chaban
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My problem is NVT crashes at step 0 and no energies or any other output
file is written...
What about visualizing your interface?
On 5 April 2013 10:25, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Hi all,
I have problem ruunning NVT with Z direction extended to get surface
But you have conf.gro
On Fri, Apr 5, 2013 at 10:29 PM, Elisabeth katesed...@gmail.com wrote:
Well I am not getting the trajectory. Simulation crashes before any step
is calculated :(
On 5 April 2013 11:20, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
My problem is NVT crashes at step 0
In systems of such kind, everything will depend on the atom of the ligand,
which coordinated by copper ion.
Perform ab initio geometry optimization and find the optimal distance. Then
adjust sigma(s).
Dr. Vitaly Chaban
There is a copper ion with four ligands in my system. I am going
Dear Qinghua -
The formal relation is diameter = pow (2, 1/6) * sigma, provided that you
have only LJ potential in your interacting subsystem.
If this is not the case, an optimal sigma can only be found iteratively.
Dr. Vitaly Chaban
On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl fantastic
that copper-ligand distance is smaller
than the sum of their sigmas multiplied by pow (2, 1/6).
Dr. Vitaly Chaban
On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl fantastic...@gmail.comwrote:
Dear Dr. Vitaly Chaban,
Thanks for the explanation. I know this equation. However, the van der
Hi, is it possible to instruct gromacs to only perform the dynamics on
half of the system or protein while ignoring the rest?
thanks
Would you explain to us why you need so exotic setup?
Dr. Vitaly Chaban
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...
I am not an expert in this question, but intuitively the bandwidth between
your two workstations will likely kill most of the anticipated performance
gain.
Dr. Vitaly Chaban
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If you do not care about the atoms, which are too far away from the region
of interest, is it not reasonable just to cut that useless part? Also,
you may want to look towards implicit solvent simulations.
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 11:35 AM, Juan Antonio Raygoza Garay
raygo
?
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl fantastic...@gmail.com 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 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
maybe even better - try to visualize it in VMD to see if the format is
correct.
Dr. Vitaly Chaban
Sir
I
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 fantastic...@gmail.com wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for concern on my research! We are going to the use
On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.com 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 vdw
, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
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
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
On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl fantastic...@gmail.com 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
On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl fantastic...@gmail.comwrote:
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 effect
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
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ability a workability of the utility. It has been tried
many times and works really perfectly.
Dr. Vitaly Chaban
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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 zero
partial charges
a simple way is x2top
Dr. Vitaly Chaban
On Mon, Apr 22, 2013 at 1:38 PM, aixintiankong aixintiank...@126.comwrote:
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 charmm
Hmmm
Aren't the keywords here charged system + PME?
Dr. Vitaly Chaban
On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:
Did you visualise the system? T in function of time? Epot in function of
time?
As a side note (not relevant for PME) the mix of nstlist = 10
The salvation is to use:
mdrun -cpi state.cpt
Dr. Vitaly Chaban
On Thu, Apr 25, 2013 at 2:37 PM, Justin Lemkul jalem...@vt.edu wrote:
Can any body tell me how do it split script i such that i will get all
20ns simulation
You specified a given time limit for the job, and the run
Aren't the keywords here charged system + PME?
Dr. Vitaly Chaban
On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:
Did you visualise the system? T in function of time? Epot in function of
time?
As a side note (not relevant for PME) the mix of nstlist = 10
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
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
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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 safasouil...@gmail.com wrote:
Dear Gromacs users ,
I did the simulation of a single molecule
I think you can process the trajectories without generating TPR.
Dr. Vitaly Chaban
On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy venkat...@gmail.com wrote:
Dear gromacs users,
I am analyzing trajectories of an ionic liquid system generated using AMBER
MD package. The force field parameters
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...@gromacs.org
electrostatic
charges for each site.
Dr. Vitaly Chaban
On Thu, May 9, 2013 at 11:33 PM, Eric Stokes es...@uw.edu 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 stearic
that it happens?
Thank you. Dr. Vitaly Chaban
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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 vvcha...@gmail.comwrote:
any ideas what the below error message can indicate?
Step 350755:
The charge group starting at atom 44257 moved than the distance allowed
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 paeanb...@gmail.com wrote:
Hi, all,
I finally wrote a decane
if there are many values in the literature, what do you want?
On Mon, May 27, 2013 at 4:29 PM, Ishwor Poudyal ishwor_p...@hotmail.comwrote:
Dear all.I want to study simulation of carbonmonoxide in water...I get
different values of force constant partial charge while searching for those
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 jeyavimala
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 revthi.san...@yahoo.comwrote:
Dear all,
I am a beginner to performing simulations and my system consists of
protein+ cholesteryl ester
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
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 gontc...@gmail.com wrote:
Hello
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 vvcha...@gmail.comwrote:
If the frame was saved
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
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
. Why don't you want to use molecular dynamics?
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 4:10 PM, Mohan maruthi sena
maruthi.s...@gmail.comwrote:
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
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 invocation line.
Dr. Vitaly Chaban
Fábio Filippi MatioliGraduando em
The force should not probably exceed kT product too much...
Dr. Vitaly Chaban
On Wed, May 29, 2013 at 3:19 PM, Sathish Kumar sathishk...@gmail.comwrote:
Dear Sir,
In pulling simulations how to set pull_rate and
pull_k .On which basis we can set these values
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
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 vvcha...@gmail.comwrote:
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
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 pmcho...@syr.edu wrote:
I'm working on a .GRO file and have
Hmmm...
And what does the observed difference look like, numerically?
On Thu, May 30, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
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
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 paeanb...@gmail.com wrote:
Hi, all,
I want
Nohow.
Numbers in GRO files serve exclusively decorative function.
Dr. Vitaly Chaban
On Tue, Jun 4, 2013 at 4:12 PM, Bao Kai paeanb...@gmail.com wrote:
Hi,
I guess the renumbering of the atoms and molecules will be a problem,
especially when the two boxes contain the same type
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 iitd...@gmail.com wrote:
Dear gmx users,
I had installed gromacs 4.6.1 using cmake. All
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 mailmd2...@gmail.com wrote:
Hello :
I am going to use Gromacs with PLUMD plugin to perform Metadynamics.
Since this methods
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 s.neuman...@gmail.comwrote:
Dear Gmx Users,
I am running CG simulation and I wish my beads to be constraint - one away
from each other of 0.4
. The
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
annealing, which you do not list here.
Dr. Vitaly Chaban
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On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul jalem...@vt.edu 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
blowing up in the sense
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 s.neuman...@gmail.comwrote:
I was not sure about the fucntion type (1
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 nshafi...@wesleyan.edu wrote:
Hi everybody,
I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman
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 hoe
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
o.rus...@fz-juelich.dewrote:
Dear Gromacs users,
I experience
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
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