, Mark Abraham
wrote:
>
>
> On Tue, Jan 20, 2015 at 8:11 PM, Dr. Vitaly Chaban
> 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 g
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
wrote:
> What can segmentation fault in g_clustsize indicate?
>
> The error occurs irrespective of which atom type for clus
What can segmentation fault in g_clustsize indicate?
The error occurs irrespective of which atom type for clustering we select.
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I believe once you have a topology (bonds...), it is easy to adapt it to
any external force field...
x2top generates topologies for nanotubes.
genbox adds water.
Other things can be done by hand.
On Fri, Dec 5, 2014 at 1:47 PM, Sergio Manzetti wrote:
> Dear all, is there a procedure with re
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 wrote:
> Dear gromacs users,
>
> I want to simulate the conformation of peptide in solution (20 monomers of
> Glutamate with solution).
On Thu, Oct 30, 2014 at 12:30 PM, Ioanna Styliari
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 number of
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 wrote:
> Dear Users
>
> I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS
> 4.5.7 single precision.
>
> My earlier work flow
> 1) T
On Thu, Oct 30, 2014 at 5:55 AM, rama david 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
> http://comments.gmane.org/gmane.science.biology.gromacs.user/51771
>
>
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 wrote:
>
>> Hi Gromacs users,
>>
>>I want to simulate a monolaye
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 Suryan
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
Вит
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, I
On Wed, Oct 29, 2014 at 6:37 PM, Agnivo Gosai 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; two coupling gr
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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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 ver
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 wrote:
>
>
> On 10/19/14 1:43 PM, Eric
0
> under [ atomtypes ].
>
>
> 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.
>
>
>
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 wrote:
> I searched the energy file made by
The assigned masses are due to the presence of dummy atoms. The model
molecule must represent moments of inertia.
1-4 (fudgeLJ and fudgeQQ) interactions do not apply for water. So, you care
about a larger molecule only.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sat, Oct 18, 2014 at 8
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 wrote:
> I am trying to transit from NPT t
I believe only writing the ITP file(s) by hand.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 15, 2014 at 5:49 PM, Victor Rosas Garcia
wrote:
> Hello everybody,
>
> I want to build a topology for a lipid to use the parameters reported
> by Jämbeck and Lyubartsev
>
> Jämbeck, Joaki
"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 wrote:
> Hi, I’m a beginner of gromacs. I want to do simulation for a protein with
> protein with ferrous or ferric. But there is no iron
I believe 2D liquid is a liquid film. If so, none of your options will work.
You need to surround the liquid film with a layer of vacuum and
simulate NVE ensemble.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 15, 2014 at 6:06 AM, Cai wrote:
> Hi users,
>
> I am trying to simulat
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
wrote:
> Hello,
>
>
> I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded
> in POPC lipid membrane. After energy
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 wrote:
> Hi. Does that mean the umbrella don't overlap enough at those z ?
> Can you make an overlay plot of the histograms of each umbr
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 wrote:
> Thanks for you reply.
>
> On a different machi
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 wrote:
> Why non-equilibrium can cause lost of total energy in NVE simulation?
> (bari
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 wrote:
> The artifacts
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 away
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 AM,
ergodic in practice. 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 Sa
What about taking another alkali ion (are thery any in CROMOS53?) and
adjusting sigma&epsilon 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. Vi
precision gromacs, the drift 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
> wr
, Antonio Baptista 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
>> wrote:
>>
>
what is it needed for?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu 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 ?
>
> If I use V-resca
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
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 wrote:
>
>
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 wrote:
> Can the gromacs simulate the growth of the molecule?
> For example, does it allow to add units to the polymer chain at
On Tue, Sep 2, 2014 at 10:59 AM, soumadwip ghosh
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 solvent viscosity and
> p
Nohow.
Because the peptide is not covalently bound to the lipid.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Tue, Aug 12, 2014 at 6:57 PM, Ozbil, Mehmet wrote:
> Hello,
>
>
> I am trying to run a GROMACS simulation with few amino acids covalently bound
> to Palmitoyl-linoleylphosphat
One MeOH molecule has run away from your PDB file.
Maybe something wrong with formatting?
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sat, Aug 2, 2014 at 12:09 AM, Deepak Ojha wrote:
> Dear gmx_users
> I am trying to do a simulation of methanol using the topology file from
> virtualch
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 wrote:
> Dear GMX
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 wrote:
> Dear gromacs users:
>
> is there any gromacs command that can allow us to compute the maximum
> allowable
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#
wrote:
> Dear Gromacs users,
>
>
> I wanted to simulate metal ions in gromacs. For Fe+2, I have lj potential
>
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 wrote:
> Hi!
> Im simulating th
You can see in the topology file whether gromacs wrote down bonds
responsible for periodicity.
Coordinate file says nothing in this regard.
Good luck.
Dr. Vitaly V. Chaban
On Wed, Jul 23, 2014 at 1:53 AM, Guilherme Duarte Ramos Matos
wrote:
> Dear GROMACS user community,
>
> I'm working
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, o
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
wrote:
> Hi dear Gromacs users, i would like to report something maybe could be a
> bug or a mistake of me , you´ll see, i run an M
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 wrote:
>
>
> On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
>>
>> Dear all,
>>
>>
>> I want to simulate graph
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
ou could explain 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
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 wrote:
> Dear GROMA
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 wrote:
> Hi,
>
> I cannot obtain the last line (box vectors *1.82060 1.82060 1.82060*) of
> the .gro file.
>
> *Can anyone expla
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 30,
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 wrote:
> Dear Users,
>
> Would you please suggest a few examples of using GROMACS to simulate an
> EDLC device?
>
> Thanks a lot!
>
> Andy
> --
;
>>
>> Charmm ff)
>>
>>
>> Hence, i would like to know how do i interpret this values in charmm27 ff
>> in gromacs? Thank you for your concern.
>> Msg: 3
>> Date: Tue, 24 Jun 2014 11:26:02 +0200
>> From: "Dr. Vitaly Chaban"
>> To:
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 wrote:
> Dear all,
>
>
> Experimentally determined charges and non-bonded interaction values for
> ligand atoms ( Writte
thermodynamic ensemble has nothing to do with an average pressure value.
Dr. Vitaly V. Chaban
On Mon, Jun 23, 2014 at 7:50 AM, Chetan Mahajan wrote:
> Dear All,
>
> I am using Berendsen barostat and thermostat for NPT equilibration MD run
> at 1 atm and 300 K. While it runs fine, average pressu
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
wrote:
> Dear Gromacs Users,
>
> I have read some articles about the more appropr
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 wrote:
> Dear all,
> I want to simulate a membrane protein system. My membrane is composed of
> DOPC (cis isomer) an
turn off your pc
Dr. Vitaly V. Chaban
On Sun, Jun 15, 2014 at 5:53 AM, Batdorj Batsaikhan
wrote:
> Dear GMX users,
>
> I am a new user of gromacs on cluster. I use putty to connect to the cluster.
> I have a problem. How to exit cluster during the simulation?
>
> My last command is " mpirun -n
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 Thu
where do you see errors?
Dr. Vitaly V. Chaban
On Tue, Jun 10, 2014 at 2:44 PM, Neha Gandhi wrote:
> Hello,
>
> I am trying to run coarse grained MD in gromacs. I get following errors,
> should I reduce the time step? Your feedback is appreciated.
>
>
> NOTE 1 [file prod1.mdp]:
> nstcomm < ns
no.
Dr. Vitaly V. Chaban
On Mon, Jun 9, 2014 at 3:36 PM, Nilesh Dhumal wrote:
> Hello,
>
> Could it possible to run the simulation with reactive force field using
> Gromacs?
>
>
> Nilesh
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Suppo
> On Jun 5, 2014 8:34 AM, "#ZHANG HAIPING#" 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 way, is it
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
wr
if you simulate adsorption of your molecule at 2 bar and then seal the
tube, then pressure inside tube will be 2 bar. in turn, you can
control pressure outside using the barostat.
though a difference between 1 bar and 2 bar in case of very spatially
small MD systems and therefore huge pressure flu
why do you need this weird setup?
Dr. Vitaly V. Chaban
On Wed, May 28, 2014 at 1:25 AM, Justin Lemkul wrote:
>
>
> On 5/27/14, 6:52 PM, ANDRES ADOLFO ORTEGA GUERRERO wrote:
>>
>> Hi Dear Gromacs Users
>>
>> I was wondering if i want to simulate a SWCNT with water inside, it
>> possible , to ru
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 helicop
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
wrote:
> Hi dear Gromacs User,
> I have done a pulling simulation of a SWCNT against an ion
I would better start from lipids containing GLY backbone then from propanol...
In any case, basic tests, such as vaporization energy & density
comparison, will be required.
Good luck.
Dr. Vitaly V. Chaban
On Sun, May 25, 2014 at 6:28 PM, Carlos Navarrro Retamal
wrote:
>
> Dear gromacs users,
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 wrote:
> Hi all,
>
>
> I have the 8-residue peptide and I want to do Molecular Dynamics
> simulations at pH 2 (with explicit sol
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. Chaban
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
On Tue, Apr 15, 2014 at 10:39 AM, Pierre THEVENET wrote:
> Hello everyone,
>
> I am using gromacs to perform a small minimization of the structure of my
> peptides, and some have aromatics rings (in tyrosines for example) . Before
> the minimization the ring is perfectly plane (CB-CG and CZ-OH bon
seems I achieved that with
1 & ! 2
Dr. Vitaly V. Chaban
On Mon, Apr 14, 2014 at 1:52 PM, Dr. Vitaly Chaban 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. C
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 mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read h
do you have your protein as a single charge group?
Dr. Vitaly V. Chaban
On Mon, Apr 7, 2014 at 11:48 AM, pratibha wrote:
> Hi all
>
> I would like to first quench my system from 500K to 300K and then do NPT
> eqilibration followed by NPT production run. But while running grompp for
> NPT eqil
So, "between" or "intra"?
"extended intramolecular bonds between cosolvent molecules"
Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 8:31 PM, pratibha wrote:
> Hi all
>
> I have done simulations of my protein in water-cosolvent system (random
> initial addition) at 450K. At the end I have used:
>
hen 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
> wrote:
>>
>> I b
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 wrote:
> Dear all,
>
>
>
> When I simulate a solution of a drug in water/methanol to study the
> self-aggregation, and try to determine the interaction ener
I believe the answer pretty much depends on how large speedup you get
with your present setup. Would you provide this info?
Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 7:14 PM, Amjad Farooq wrote:
> Hi everyone,
>
> I am running Gromacs 5.0-beta on a remote workstation (next door) from my
> P
Exactly. So is there any chance to circumvent the problem?
Function type Fourier Dih. not implemented in ip_pert
Dr. Vitaly V. Chaban
On Mon, Mar 31, 2014 at 5:49 PM, Justin Lemkul wrote:
>
>
> On 3/31/14, 11:35 AM, Dr. Vitaly Chaban wrote:
>>
>> Since I do not
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
nstdh
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 wrote:
> Program mdrun_mpi, VERSION 4.6.2
> Source code file:
> /gromacs-2014.01.14-12-21-22-nbreLi.itsi/gromacs-
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 y
>> > 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 U
you request.
>
>
>
> 2014-02-23 22:21 GMT+01:00 Dr. Vitaly Chaban :
>>
>> 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
Strange.
Sometimes things like this may happen if you incorrectly treat
periodicity between runs.
Without having the system at hand, I cannot say more.
Dr. Vitaly V. Chaban
On Thu, Feb 27, 2014 at 8:16 AM, gupta.rakesh082
wrote:
> EM RUN
>
> Steepest Descents converged to machine precision i
editconf -box X Y Z
Dr. Vitaly V. Chaban
On Wed, Feb 26, 2014 at 7:58 PM, decaiyu 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 vaccum thi
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 wrote:
> Dear Gromacs users,
> we want to simulateHSA protein using8 processors. Usually with our available
>> 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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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_L
ms, it is probably worthwhile to estimate system density in
certain manner and then proceed with it in the NVT.
Dr. Vitaly V. Chaban
> On Tue, Feb 25, 2014 at 6:48 AM, Dr. Vitaly Chaban wrote:
>> in that case the average is reasonable, but you should state in the
>> manuscript
worked fine there
>> with the average pressure at 5.15bar.
>
>
> Sujith.
>
>
> On Tue, Feb 25, 2014 at 2:29 PM, Dr. Vitaly Chaban
> wrote:
>>
>> your average pressure is the pressure you should report in the
>> publication. if you got 5 bars instead of 1
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 . wrote:
> On Mon, Feb 24, 2014 at 5:37 AM, sujithkakkat .
>
sorry, and what performance did you expect from REMD?
Dr. Vitaly V. Chaban
On Mon, Feb 24, 2014 at 8:32 AM, Singam Karthick 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 with the exchan
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 V. Chaban
On Sun, Feb 23, 2014 at 9:04 PM, Marcelo Depólo wrote:
> Justin, as far as I rea
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 wrote:
> Still about the question of temperature coupling with method of the
> periodic perturbation I have the f
There is such thing in simulations as energy conservation...
If you use "vdwtype= cut-off" and this cut-off happens at 0.8nm, while
sigma for the largest atom is ~0.34nm, the problems are inevitable.
Your cut-off should not be smaller than 0.90nm, and you need to apply
a more polite method to bri
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 wrote:
> Maybe I should explain it better.
>
> I am using "*mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o prt.trr*", pretty
> much a
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