Dear Prema:
1. Do you think my e-mail is an alias for gromacs mailing list, please? I am
not sure.
2. What about downloading the manual and referring yourself to the section
where topology files are described?
Enjoy gromaxing...
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ
mpatibility error, like /"There is
> no domain decomposition for 7 nodes that is compatible with the given
> box and a minimum cell size of 0.95625 nm"/, but for example 6 or 8 cpus
> give a successful run).
>
> Can anyone understand what is the reason of this strange behavi
Writing checkpoint, step 1390010 at Thu Jan 19 12:21:23 2012
Writing checkpoint, step 1390020 at Thu Jan 19 12:21:28 2012
Writing checkpoint, step 1390030 at Thu Jan 19 12:21:32 2012
The job is executed using 4 cores. The version is 4-0-7.
Is this a bug? Just curious.
--
Dr. Vitaly V. Chaban, 430
collision
for the particles approaching it.
There was some discussion of this matter in this list around
February-March, 2009, browse archives...
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
> Dear All,
>
> Suppose I need to install the GROMACS in my laptop. Will you please tell me
> the requirement on the capacity of RAM?
>
I still did not invent a system that would not run on my 8GB RAM laptop.
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Roche
imulated annealing)
> (If yes then what the temp. should I have to used for NVT and NPT
> (as in mdp file has lower 5 K and high 300 k ) )
>
Your system will be heated from 5 to 330K during 20ps. If this is what
you want, than it is correct. I would, however, prefer slower heating
in or
Dear All --
I have a system of the liquid/vapor interface kind. The droplet of
liquid with a radius of about 10nm is surrounded by a volume of vacuum
of ~1000nm^3. What is the best method among those currently in
GROMACS4 to treat electrostatics in this case?
Dr. Vitaly V. Chaban, 430 Hutchison
= no
> optimize_fft = no
> constraints = hbonds
> constraint_algorithm = Lincs
> *
This discussion should be started with you reporting the speedup for
your system with 200cpu's. Rather than appealing just to some velocity
per nanosecond.
Neighbo
ke CaO or MgS.
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Please search the archive at
http://www.gr
re not involved in H-bonds, the
coordinates of the remaining atoms will be optimized. Another question
is why you need that "before building a solvent".
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
--
accuracy anyway.
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Please search the archive at
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lieve the only way is to construct the index file by hand.
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Please sea
43 2012
> vol 0.50! imb F 11% pme/F 0.57 step 2300, will finish Sat Apr 14
> 19:13:30 2012
> vol 0.49! imb F 11% pme/F 0.57 step 2400, will finish Sat Apr 14
> 19:10:14 2012
> vol 0.48 imb F 10% pme/F 0.58 step 2500, will finish Sat Apr 14
> 19:01:51 2012
> vol 0.47! imb F 12% pm
;parrinello-rahman
> Pcoupltype = semiisotropic
> tau_p = 1.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
> pbc = xyz
> refcoord_scaling = com
> gen_vel = no
> opt
converge
faster. What is the shear viscosity of octanol, something around 5-10
cP?
Regards,
Vitaly Chaban
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
> I prepared a box of 12
em.
> (I mean building different binary systems with different mass
> fractions of w, and measuring average P (dP/dw) while keeping T and V
> constant does not produce meaningful results by MD)
I think you have just to increase sampling to get trustworthy
pressures for a range of your syst
Dear Ahmed -
I do not understand how you imagine "FCC geometry" in the liquid state
of matter.
If you want to just resize my system, use the standard "genbox"
utility and then re-equilibrate at the desired temperature and density
(if you want to fix density, of course).
y, isn't it?
>
>
> ________________
> De : Dr. Vitaly V. Chaban
> À : ahmed sta
> Cc : gmx-users@gromacs.org
> Envoyé le : Vendredi 25 mai 2012 18h15
> Objet : Re: Re : Re : Gromacs
>
> Writing your program has nothing to do with gromacs. If you do not
> have experience i
based on the fact
that the density of the liquid phase (in the NPT ensemble) is not
ideal.
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
On Fri, May 25, 2012 at 10:44 AM, ahmed sta wrote
see
>
> I think that writing my own program would be better and more accurate
> How should i proceed ?
> it is my first use of Gromacs and i do not know how to do
>
> Regards
>
> ____________
> De : Dr. Vitaly V. Chaban
> À : ahmed sta
> Cc
Ahmed -
This is *YOUR* research, not mine. I believe I have given you enough
hints to succeed.
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
On Fri, May 25, 2012 at 12:51 PM, ahmed sta
es of some models?
>
There should be a file with polarizable water topology in the standard
topology folder of the gromacs installation.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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gmx-users mailing
1 3 4 5
3 1 2 4 5
4 1 2 3 5
5 1 2 3 4
#ifdef POSRES
; Restrain the oxygen...
[ position_restraints ]
; iatom typefx fy fz
1 1 100 100 100
#endif
===
4, 25, 26 are the group
> numbers in index file.
>
As always in linux scripts.
g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize << EOF
25
EOF
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES
> I would like to know your idea and comments on methods 1b and 2a.
>
> Appreciate your comments.
>
What is your system?
(1a) is what everyone does.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
On Wed, Aug 3, 2011 at 3:17 PM, Elisabeth wrote:
>
>
> On 2 August 2011 15:29, Dr. Vitaly V. Chaban wrote:
>>
>> >
>> > Hello,
>> >
>> > I wanted to know your ideas on calculation of heat of vaporization using
>> > a
>> > sin
I wonder how you know that your polymer chain in computer is exactly
your polymer chain in experiment Of course, the difference of
vaporazation enthalpy per mole is to be observed. You may guess, may
not guess, but method is not guilty if you may not.
--
Dr. Vitaly V. Chaban, 430 Hutchison
>
> I want to simulate system with 128 ionic liquids (128 cation+128 anion).
>
> I have made a pdb file with a single ionic liquids ion pairs.
>
> How can I genrate 128 ion pairs using single ion pair .pdb file.
GENCONF
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dep
> Thank you. I am looking at potential energies to calculate vaporization
> heat. I wanted to know how the fact that berendsen does not lead to correct
> ensemble is affecting total potential energy of the system
Nohow.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ.
What criterion does the grompp utility use to identify H-atoms when it
is requested in the MDP file to apply constraints=h-bonds? Thanks.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
--
gmx-users mailing
Thanks! That's reasonable.
On Fri, Aug 19, 2011 at 2:31 PM, Bogdan Costescu wrote:
> On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban
> wrote:
>> What criterion does the grompp utility use to identify H-atoms when it
>> is requested in the MDP file to apply cons
version is 4.0.7 used with OpenMPI.
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Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Please search the
In the below issue, the barostat is setup semiisotropically and works
only along the "long" direction. The density of the system slowly
grows due to mixing. If this can be useful
On Mon, Aug 22, 2011 at 5:32 PM, Dr. Vitaly V. Chaban
wrote:
> We are running the system consis
>
> On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaban wrote:
>> In the below issue, the barostat is setup semiisotropically and works
>> only along the "long" direction. The density of the system slowly
>> grows due to mixing. If this can be useful
>
> Do
on. But it is interesting where it is anyway.
Interestingly, if I retrieve the last configuration before crash from
the TRAJ.XTC and start from it, initializing velocities again, it
passes the old crash point. If I start from checkpoint, it crashes.
Vitaly
> On 23/08/2011 8:44 AM, Dr. Vitaly V. Chaba
On Mon, Aug 22, 2011 at 9:02 PM, Dr. Vitaly V. Chaban
wrote:
>> Your density seems to be about 70% of what I would expect. Are you
>> sure that this is not just a normal case of a poorly equilibrated
>> system crashing? That matches with what you say about the density
>> g
>> Does a different barostat work?
No. Switching to Berendsen barostat did not help.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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tical
Chemistry", 116, 206 (2006).
5. C. F. Craig, W. R. Duncan, O. V. Prezhdo “Trajectory surface
hopping in the time-dependent Kohn-Sham
theory for electron-nuclear dynamics”, Phys. Rev. Lett., 95 163001 (2005)
===
--
Dr. Vitaly V. C
nded because these atoms are not directly
bound. They are separated by 3 chemical bonds, yet belonging to the
same molecule.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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you should NOT include this term.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Please search the archiv
On Fri, Aug 26, 2011 at 3:12 PM, Juliette N. wrote:
>
>
> On 26 August 2011 13:25, Dr. Vitaly V. Chaban wrote:
>>
>> >>. Now it is clear that
>> >> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials.
>> >> Thank
>> >&
us messages. There
> may be other terms if PME was not used.
Of course. These four are just an example for the most traditional
setup for periodic boxes with electrostatics.
>>
>>
>>
>>
>> On Fri, Aug 26, 2011 at 3:12 PM, Juliette N.
>> wrote:
>>
And the charge number in [ atomtypes ] are always 0.0.
> Which one is actually read by gromacs program ?
That one which is mentioned the last
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
--
g
On Wed, Aug 31, 2011 at 8:23 PM, Justin A. Lemkul wrote:
>
>
> Dr. Vitaly V. Chaban wrote:
>>>
>>> Hi, ALL
>>>
>>> I have a question about the charge defined in the topology file.
>>> It seems to me that the charge for each atom ap
still has a non-zero total charge:
> System has non-zero total charge: 5.70e+01
>
63 non-compensated ions in the single system... I wonder what this system is
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AM
/force arises in order to get back to the equilibrium.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
> Dear users,
>
> I have a short question about temperature dependence of enregy terms i.e
> b
Justin, I was speaking only about the bonded (and presumably,
harmonic) potentials. Decreasing the time-step, as I mentioned, never
made the things worse.
Vitaly
On Tue, Sep 6, 2011 at 7:59 PM, Justin A. Lemkul wrote:
>
>
> Dr. Vitaly V. Chaban wrote:
>>
>> Hello J
Cool... :-)
> Hi,
>
> for your entertainment and as a reach-out to younger scientists GROMACS
> is now on Facebook. Please look us up at:
>
> http://www.facebook.com/pages/GROMACS/257453660934850
>
> We're looking forward to your comments.
>
> Cheers,
> --
> David van der Spoel, Ph.D., Professor o
rature of largest cluster"
@xaxis label "Time (ps)"
@yaxis label "T (K)"
@TYPE xy
---
The invocation line is: g_clustsize -n index.ndx
Did anybody see this function working? I am using 4.0.7
he code. CTRL+C/V solves the problem.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Please search th
If the [ defaults ] sections are identical, you have just to add the
items from [atoms], [bonds], etc sections of the new force field to
the appropriate sections of the old force field.
The compatibility of these force fields is a sort of magic that is up to you.
- Vitaly
> I have a general que
our results, you will need to
exactly specify the number of monomers in your chain. It may also be
interesting to discuss how much your properties are affected by this
length.
> And usually properties depending on Mw level off with no significant change
> in the property of interest vs chain l
Hello Ahmet:
The warnings originating from the LINCS algorithm are dee to either
incorrect topology (TOP file) of certain particle or bad initial
configuration (GRO file).
If you don't provide this information about your problematic system,
there is no chance to help you.
--
Dr. Vit
ahmet yıldırım:
If you want a personal mentoria, you will need to pay for it first. If
you strive to get a FREE help, all correspondence should be kept in
the mailing list to save up an archive for other gromacs users.
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester
You should provide topology file, I do NOT need your MDP files.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
2011/10/31 ahmet yıldırım :
> Dear Dr. Chaban,
>
> Firstly, thanks for your reply. I
gt; option in both of that software but couldnot find
>
>
> Thank you for your help,
>
> James
Among free solutions... maybe this would help:
http://www.chemaxon.com/marvin/sketch/index.php
I don't know molecular editor plugins for VMD, but it would be cool,
if one is accessib
u should increase table-extension in your mdp file
> or with user tables increase the table size
I think your system is not relaxed, so you are NOT actually running
"production md".
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-02
Could anybody please suggest a convenient compressibility value for MD
boxes of gases (at normal conditions)?
Thanks.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Looks generally reasonable. Thanks! - Vitaly
On Tue, Nov 8, 2011 at 12:20 PM, Krzysztof Kuczera wrote:
> The ideal gas result is -(1/V)(dV/dp)_T = 1/p , so I suppose the value
> should be = 1.0 bar-1
> under standard conditions
> Krzysztof
>
> On 11/8/11 10:51 AM, Dr. Vita
cannot be just a result of large fluctuations.
Thanks in advance.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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he density is reproduced
adequately in both ensembles.
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Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Please sea
ain cases
(e.g. when velocities or forces should be analyzed), this is not
perfect, of course.
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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sed if anyone could help me how to fix this.
Maybe the non-found atomtype is really absent? On the gromacs website,
there should be some examples for the CNT topologies based on the
GROMOS FF.
Independently, check your angles once again. It seems, there should be
more angles which are to be de
t taken care of.
>> >
In periodic system, there is infinite number of images of each
particle. You should always consider the smallest possible distance
[between the image of the two particles].
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester,
Zahra:
I believe the problem is in your topology (*.TOP) file which you don't
attach. From your pictures, we see that the system does not survive
energy minimization, so the intramolecular interactions are not
simulated wisely.
Happy New Year,
Dr. Vitaly V. Chaban, 430 Hutchison Hall,
f you don't need a flexible tube, you
can just freeze its carbon atoms (in the MDP file), so that the
geomerty will be stable at all times
--
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
On Sat, Dec 31,
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