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
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
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
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
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).
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
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
;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
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
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
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
http://www.gro
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
--
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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= 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
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
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,
>
> 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
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
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
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
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,
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,
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,
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
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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he density is reproduced
adequately in both ensembles.
--
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
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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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
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
--
gmx-users mailing listgmx-users
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
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
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
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
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
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
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
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
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
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
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
/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
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
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
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
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:
>>
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
>> >&
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
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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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
>> 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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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
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 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
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
version is 4.0.7 used with OpenMPI.
--
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
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
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
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> 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.
>
> 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
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
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 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
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
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
===
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
--
gmx-users mailing
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
>> Hello, I want to set the density of the box (e.g. set 1 g/ml for
>> the water box). I use the density option in the editconf, then use the
>> genbox to generate the box, but the result of the density is not what I
>> setted. How can I do ?
It seems to be much easier in your case to calcu
> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
> Generated 837 of the 2346 non-bonded parameter combinations
> ---
> Program grompp, VERSION 4.0.5
> Source code file: toppush.c, line: 947
> Fatal error:
> Atomtype OS not fo
Hi all,
Does anybody have a script translating CPMD trajectory into gromacs XTC and
TRR files?
Thanks.
Dr. Vitaly Chaban
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>> Hi, everyone
>>
>> I have two simulations which could run well separately. Now I want to place
>> the box of simulation A onto the box of simulation B. What should I do to
>> realise that?
>>
>> I've tried to copy and paste the .gro and .top file together, but there are
>> several mistakes in gr
Yeah... You are a spammer however.
I do not see the command you type.
On Thu, Mar 25, 2010 at 7:26 PM, Moeed wrote:
> Hello,
>
> Recently, I have started my PhD at McGill and I am a new user of GROMACS. I
> am trying to run x2top command to generate topology file but I am getting
> the followin
On Thu, Mar 25, 2010 at 12:45 AM, XAvier Periole wrote:
>
> On Mar 24, 2010, at 10:58 PM, Vitaly V. Chaban wrote:
>
>>> Hi,
>>>
>>> I want to test different values of cutoff for vdw. However, in the list
>>> someone said cutoff = 0.9 for vdw was used
> Hi,
>
> I want to test different values of cutoff for vdw. However, in the list
> someone said cutoff = 0.9 for vdw was used for paramaterizing of >Gromos
> force field, other values would cause error, and also there was someone
> saying that cutoff for vdw should be set to 1.4. Can >someone m
Charges... Hmmm...
I think you have incorrect data types passed to x2top.
Vitaly
>
> I think the result cannot be trusted because the total charge is 1.2, which
> seems impossible. I just used the result calculated by Material Studio and I
> used the value of charge on the internal atoms. The at
And how will protein and carbonate interact with one another according
to your model?
Look towards tabulated potentials - with them you can perform any miracles. :)
--
Dr. Vitaly Chaban
http://chaban.at.ua
> I would like to use gromacs-4 to do a simulation of a small protein in water
> and in
e it worked :-)
> But the result cannot be trusted.
>
> Di Cheng
>
> University of Science and Technology of China
> Hefei, Anhui Province 230026
> P. R. China
> E-mail: chen...@mail.ustc.edu.cn
> Tel.: +86-15321055911
>
>
>
> On Tue, Mar 23, 2010 at 8:10 PM,
Try to use the following:
x2top -f SiO2.pdb -o SiO2.top -name SIO2 -ff oplsaa -pbc
--
Dr. Vitaly Chaban
http://chaban.at.ua
>
> Hi, everyone
>
> I've just tried x2top.
>
> My ffoplsaa.n2t file is as follows
>
> ;atom atom_type charge mass neighbor_N neighbor
> distance
> O
Hi,
Is there any example systems to test gromacs/mopac interface?
Thanks.
Vitaly
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5 1
> 4 1 5 1
>
> My RDF does look reasonable and the peaks are okay with the values
> published earlier, but because of what I am calculating (i.e. volume),
> it seems to be very sensitive and even 0.01 makes a difference.
>
> Thanks for suggestions.
>
>
>
> I am trying to get an rdf graph actually, and my values are very close
> to one, but not exactly one, and I was wondering if there is some
> normalization issue with g_rdf? These are my values for rdf:
>
> 0 0
> 0.002 0
> 0.004 0
> 0.006 0
>
ential has been taken to be harmonic. Any knowledge of related literature
> would be helpful because I could not find by googling.
>
> Your idea will really help me.
> Neal
Many guys enjoy SPCE. Its diffusion constant is lower than those of
the models you mentioned, if I'm not
> Hi
>
> what is the best program and force field for md simulation of carbon nano
> tubes?
There's no such one as for me.
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0.14 F 0.14 F 0.14 S 0.18
O O 1 S 0.17
Vitaly
On Fri, Feb 5, 2010 at 10:13 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul wrote:
>>>
>>> Vitaly V. Chaban wrote:
>>>>
On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> In this context, it is interesting how X2TOP decides that two atoms
>> are connected? Only on the base of N2T: if the atom should have 4
>> neighbours, it looks f
?
-- Forwarded message --
From: Vitaly V. Chaban
Date: Fri, Feb 5, 2010 at 7:56 PM
Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for
atom S (2) with 3 bonds
To: jalem...@vt.edu, gmx-users@gromacs.org
Yes. This worked even with my N2T. I will probably recreate my PDB...
On Fri
Yes. This worked even with my N2T. I will probably recreate my PDB...
On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Justin,
>>
>> Am I correct that X2TOP uses only N2T file to make a topology?
>>
>
> Yes.
utput... This is like it has predefined Sulphur with 3 bonds.
Vitaly
On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban wrote:
> Hi,
>
> This can be the reason when X2TOP gives the following error:
> "
> Fatal error:
> No forcefield type for atom S (2) with 3 bonds
> "
&
.172
F F 1 C
The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
3. If I change the string in the N2T to 3 bonds, the topology is
generated but S-C bond is absent.
What can be the problem?
Thanks.
--
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.ht
se the units
> associated with the different kinds of interactions.
>
> Erik
>
> Vitaly V. Chaban skrev:
>>
>> Hi,
>>
>> In what units does gromacs MD engine treats harmonic bond constants?
>> In the tutorial, there is a hint about fourth-power potenti
existing FFs (.../top/) including GROMOS96
they appear in [kJ/mol/nm^2].
If the own FF is used, in what units should one type the values of k_b
in topology file for GROMPP to understand it correctly? My variant is
[kJ/mol/nm^2]. Please let me know if I'm true.
Thanks.
--
Vitaly V. Chaban, Ph.D.
Hi Catarina,
This file contains the parameters for MD run, e.g. timestep, number of
steps, etc.
Good luck with IL,
Vitaly
--
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
On Thu, Feb 4, 2010 at 2:39 PM, Catarina Nunes wrote:
> Sorry Vitaly,
> Can you tell m
> Dear all,
> Do you have any tutorial for ?
> Best regards
> Catarina
I have worked with MD of RTILs quite a lot. So if you have got
concrete questions, you can probably ask me directly.
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
--
gmx-users mailing
>
> This updating is very infrequent. Usually one sees a value of 5-10 here
> (usually 5 for Gromos96). If your neighborlist is updated infrequently, you
> can
> have problems (poor energy conservation and perhaps incorrect calculation of
> interactions). Perhaps this is why your short timestep
===
On Mon, Jan 25, 2010 at 10:27 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>>
>>> 1. No problem at all in vacuo? That with a 1 fs timestep and the sd
>>> integrator? Strange then that your molecule is ok and the wa
> 1. No problem at all in vacuo? That with a 1 fs timestep and the sd
> integrator? Strange then that your molecule is ok and the water is ok,
> but they are unstable together. Perhaps your'e not getting any LJ
> interactions (or not correct ones) between your solute and water? That's
> where I wou
Dear Chris -
> 1. put a single solute in a large vacuum box and use the sd
> integrator. Can you reproduce the problem?
No problem in vacuo found.
> 2. Remove the dihedral parameters entirely. Can you reproduce the problem?
The problem appeared between carbon and hydrogen 1-4 atoms... Would
you
> You said before:
>
> "> > 5. What does your .top look like? (does it list the organic molecule
> > > only once in the [ molecules ] section?)
>
> Only once."
>
OK. We misunderstood one another. I meant "CIP is mentioned only once"
= "one string with CIP molecules number". So this entry was not
On Sun, Jan 24, 2010 at 8:39 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>>
>>> There's your problem (although in a different manner than I thought).
>>> If you have, for example, 3 solutes, then you should have
>>>
>>>
..
> and I'm not sure what happens to those other c2/c3.
>
I do not know also. :) This is just what was generated by X2TOP. I
tried to use only one constant instead but it didn't solve the
problem.
> Quoting "Vitaly V. Chaban" :
>
>> Hi Chris,
>>
>>
Hi Chris,
> 1. Is your system is properly minimized
Of course, it is, based on the energy values.
> 2. If you take the output from a 500 ps run with 0.25 fs timestep and
> start a 1 fs timestep run, is that new run stable?
Unfortunately the new run also crashes. The crash may be at the very
end
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