my first
> thread. In the attachement I am sending you all the files needed for the
> simulation, maybe you'll find the problem.
>
> I haven"t mentioned but we try to constrain the angles by adding fictious
> bonds. Maybe there is something wrong with this...
>
> Than
ion), the simulation crashes immediately:
>
> Range checking error:
> Variable n has value 7. It should have been within [ 0 .. 7 ]
>
> If you want to test the topology on one single ion pair, you can find a
> configuration in the attachement.
>
> Thanks in advance,
> Best,
> I am having problems in carrying out a NPT equilibration of my system at 500
> K.
>
> System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid
> anion.
>
> NVT equilibration gives expected results.
>
> When I load the npt.gro file in VMD, its seems as if the molecules have
> fragm
> Hello,
>
> I think it would be very good to have this feature in gromacs. In fact I've
> recently had some problems with constraining some species in my simulations.
> Finally I've sorted out with shake but your solution seems to me less
> problematic.
>
> Thanks in advance.
> Best,
>
> Gyorgy
>
>
> Dear all,
>
> I figured out the problem. Error was in my mdp file options. I did not
> specify the acc-groups correctly. I can get 1/viscosity using g_energy.
>
> However, once the acc-groups are specified, now the NEW issue is not being
> able to run my job correctly.
>
> I get the following e
>
>
> I am trying to create an ionic-liquid system comprising of
> 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have
> generated the system using following command:
> genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb
> , well it created syst
>
> To do this at first I fill my box using "genbox" with one of the liquids as
> solvent: I used -cs and I did not used -cp.
> and then I used "genbox" again to add the other liquid in it: first liquid
> as a solute and the second one is as solvent. But these two liquids gives
> me
> a solution. I
Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
> On Mon, May 2, 2011 at 6:10 PM, Vitaly Chaban wrote:
>
>> To do this at first I fill my box using "genbox" with one of the liquids
>>> as
>>> solvent: I us
>
>
> Hi
>
> I want to build my simulation box as tutorial. However I change
> "vdwradii.dat" file according to the tutorial liquid 2 mix with liquid 1.
> What should I do?
>
Your question is not clear.
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New Yo
>
>
> I have been trying to use CHARMM forcefield to simulate 1000 molecules
> of Methanol in a box but I seem to fall short on the density every
> time I run. At first, I had my rlist at 1 but CHARMM recommends
> greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
> that the sh
Where are your LJ parameters?
Are you sure that Tsuzuki uses all standard OPLS parameters?
What density do you get in your simulation?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
On Mon, May 2, 2011 at 1:59 AM, Prema Awati wrote
> The last time I had performed this with nstlist=5 and for the
> actual MD run, I had a density of approximately 0.781 g/cm3 compared
> to literature value of 0.791 g/cm3 at 298K.
So, what is the problem? It is satisfactory coincidence.
--
Dr. Vitaly V. Chaban, Department of Chemistry
Univers
It is not clear what is wrong with your system without checking the things
throroughly.
Therefore,
1) double-chack your topology.
2) submit longer MD simulation.
3) double-check the temperature which is requested in the MDP file.
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of R
Hey,
Could anybody share the executable of gromacs 4.X.X for windows, please?
On a related note, if the procedure of compilation is available, why not to
put the resulting executable(s) for download?
http://www.gromacs.org/Downloads/Installation_Instructions/Windows
--
Dr. Vitaly V. Chaban, De
On Thu, May 5, 2011 at 7:23 PM, Peter C. Lai wrote:
> On 2011-05-05 03:22:14PM -0500, Vitaly Chaban wrote:
> > Hey,
> >
> > Could anybody share the executable of gromacs 4.X.X for windows, please?
> >
> > On a related note, if the procedure of compilation i
>
> I got .itp and .pdb files of sulfate ion from PRODRG. I add it as an extra
> molecule (in genbox using -ci) my simulation box. I can see it visaully by
> VMD in my system. but it is not in topol.top and when I want run my program
> I receive the following error:
>
> "No molecules were defined i
Does anybody know the reference for TIP4P water, which is supplied
in tip4p.itp in the /share folder, please?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailm
> On 2011-05-09 20.19, Vitaly Chaban wrote:
> > Does anybody know the reference for TIP4P water, which is supplied
> > in tip4p.itp in the /share folder, please?
> >
> > --
> > Dr. Vitaly V. Chaban, Department of Chemistry
> > University of Rochester, Roch
I have a pure linux question. When using g_current and trying to
redirect its output to the file, e.g.
g_current -temp $TEMPER -b $conduct_b -e $conduct_e << EOF >> output
0
EOF
only a part of output is written to the file ("output")
Here is what is actually written to the file:
Selected 0: 'Sy
Thanks, Justin! Great solution.
On Tue, May 10, 2011 at 12:57 PM, Justin A. Lemkul wrote:
>
>
> Vitaly Chaban wrote:
>>
>> I have a pure linux question. When using g_current and trying to
>> redirect its output to the file, e.g.
>>
>> g_current -temp $TE
he stderr was
> that you have the ability to sort it during the analysis. However as
> Justin mentionen >& will write all open pipes into one file.
>
> Cheers,
> Flo
>
> On Tue, 2011-05-10 at 13:16 -0400, Vitaly Chaban wrote:
>> Thanks, Justin! Great solution.
>&
> the equlibration file I used
>
> title = cpeptid position restraining
> cpp = /usr/bin/cpp
> constraints = none
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 100 ; total 1.0 ps.
> nstcomm
>
> For vacuum systems, "pbc = no" in conjunction with zero cutoffs is correct
> to obtain a gas-phase system.
For reasonably large box, this is the same heck.
Nilesh: visualize your system, using VMD or ngmx. The behavior of your
molecular cluster during the first ps will provide an answer. Are
Very good.
Have you take a moment to define the box in the GRO file?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
On Thu, May 19, 2011 at 4:05 PM, Nilesh Dhumal wrote:
> if I set pbc=xyz in energy minimization mdp file then I get
> I run the same mdp files for glucose in vaccum.
>
> I ma geting the proper results, I can visualize the strucutre properly in
> VMD.
>
> If I use same for water why I am not geting proper structure ?
>
> Nilesh
Observe the evolution of energy for your water, after all.
--
Dr. Vitaly V. Chaba
> When I use constraints for all-bonds and dt of 0.002 compressing the box
> works well and I get density of above 600 SI which is the actual density of
> alkane. Can any one help why setting no constraints and dt=0.001 leads to
> the error message shown above. When no constraints is used PR doesnt
Incredible!
On Mon, May 23, 2011 at 11:40 AM, Elisabeth wrote:
> Thanks for your hint. Employing a 0.5 fs timestep resolved the problem.
>
> On 20 May 2011 22:58, Vitaly Chaban wrote:
>>
>> > When I use constraints for all-bonds and dt of 0.002 compressing the box
&
Because when you introduce constraints, you change the model. Why is
it strange for you, I would ask.
Meanwhile, the difference is comparable with RMSD.
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
> Dear experts,
>
> I have been c
Andrew,
Look here: http://www.sciencedirect.com/science/article/pii/S0022286004002765
I believe the VACs there are the same that you've showed us. So, you
are on the safe side, as for me.
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
Generally, hydrogen-bonded liquids exhibits more complexed velocity
autocorrelations than others... I recollect something like that,
working with methanol.
On Mon, May 23, 2011 at 4:23 PM, Vitaly Chaban wrote:
> Andrew,
>
> Look here: http://www.sciencedirect.com/science/ar
>
> Hello,
>
> I have calculated the velocity autocorrelation function of OH bond
> in glucose molecule. For this calculation I modified the index file. The
> modified part is pasted below.
>
> [ O10 ]
> 10 20
>
> 10 is oxygen no. and 20 is oxygen.
>
> I used following command to calculate the v
-0216
On Fri, May 27, 2011 at 8:07 AM, Nilesh Dhumal wrote:
> 20 is hydrogen atom.
> Sorry its typing mistake.
>
> Nilesh
>
> On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote:
>>>
>
>>> Hello,
>>>
>>>
>>> I have calculated the ve
xygen and then
> calculate the autocorrelation function?
>
> Nilesh
>
>
> On Fri, May 27, 2011 8:11 am, Vitaly Chaban wrote:
>> It does not change the situation, I believe.
>>
>>
>> What is the sense of calculating such ACF? In order to understand the
>>
Hmm...
1. The background of the task is not quite clear for me.
2. Evidently, the fluctuations are higher than the difference for your
pressures.
3. Why not to use significantly larger systems and significantly
larger difference between pressures?
--
Dr. Vitaly V. Chaban, Department of Chem
Either a tighter pressure coupling time...
On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban wrote:
> Hmm...
>
>
> 1. The background of the task is not quite clear for me.
>
> 2. Evidently, the fluctuations are higher than the difference for your
> pressures.
>
> 3. W
>
> Is it possible to globally scale all non-bonded interactions by a factor ? I
> know there are energy exclusion groups, but that is an all or nothing
> approach, while I would like to reduce non-bonded interaction potentials to
> e.g. 10% of their normal value.
>
> If this is not possible, I
Doesn't increased temperature work for this purpose?
On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul wrote:
>
>
> Vitaly Chaban wrote:
>>>
>>> Is it possible to globally scale all non-bonded interactions by a factor
>>> ? I know there are energ
30
>
> ; Velocity generation
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
> ; Bonds
> constraints = all-bonds
> constraint-algorithm = lincs
>
>
>
>
>
>
> On 1 June 2011 14:59, Vitaly Chab
>
> You had helped me earlier on calculating the heat of vaporization of
> methanol and it worked great. I'm just trying hard to understand
> conceptually what is the difference between simulating a liquid phase
> and a gas phase in Gromacs. I mean technically if we throw in 1000
> molecules of c
nt you ( and Dr. Chaban) this message on your personal
> account.
>
> Best regards,
>
> On 2 June 2011 22:40, Justin A. Lemkul wrote:
>>
>>
>> Elisabeth wrote:
>>>
>>> Hello Dr. Vitaly Chaban,
>>>
>>> Thank you. I asked a friend in ou
> Dear all,
> I need to create a starting pdb file for doble walled Carbon
> nano tube of desired radius with two graphene sheets.I already have one but
> when i use pdb2gmx gromacs The pdb file looks something like this..
>
> RYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1
Hi all,
Sorry for my a bit off-top message. Does anybody know the force field
model for water (polarizable/non-polarizable) that can reproduce the
temperatures of liquid freezing/evaporation? For other common liquids,
such models are also of interest. Thanks a lot. ~Vitaly
--
Dr. Vitaly V. Chaban
Hi all,
This is just to announce the post doctoral positions available in the
University of Rochester, Rochester, NY, United States -
http://chem.chem.rochester.edu/~prezhdo_group/PostdocAnnouncement_Prezhdo.pdf
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, N
> Message: 2
> Date: Wed, 22 Sep 2010 12:07:27 -0600
> From: Paymon Pirzadeh
> Subject: [gmx-users] rotational correlation function
> To: gmx-users@gromacs.org
> Message-ID: <1285178847.11669.66.ca...@paymon-desktop>
> Content-Type: text/plain
>
> Hello,
> Imagine if the total correlation function
ention.
>
> Paymon
>
>
> On Wed, 2010-09-22 at 19:03 -0400, Vitaly Chaban wrote:
>> > Message: 2
>> > Date: Wed, 22 Sep 2010 12:07:27 -0600
>> > From: Paymon Pirzadeh
>> > Subject: [gmx-users] rotational correlation function
>> > To: gm
On Wed, Sep 22, 2010 at 7:47 PM, Paymon Pirzadeh wrote:
> Well, I found a paper: J. Chem Phys. Vol. 131, 155103 (2009) in which
> they have used GROMACS and its utilities to calculate the correlation
> functions I need, however, it is not clear to me what utilities were
> used and what steps were
Hi all,
Is it possible to compute local pressure in gromacs (e.g. according to
Hoover et al., 1991)?
Thanks in advance.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
gmx-users mailing listgmx-users@gromacs.org
h
Hi all,
Could anybody please suggest "a good method" for electrostatics for
non-periodic system simulation -> PBC=no ? Let's say it is pure water
system.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
gmx-users mailin
Dear Anil:
If the charge is integer, I believe this depends only on your protein,
and you are the only one who knows the answer. If the charge is not
integer, then these are rounding errors.
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United S
Hi all,
Is there a trick in gromacs to exclude some particles from the
pressure calculation procedure? E.g. to get partial pressure(s)...
Thank you!
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America
--
gmx-users mailing li
Hi all,
Please suggest me what is the reason for the below situation.
The 1728 TIP4P waters system was simulated in NPT under 1bar
maintained with Parrinello-Rahman barostat at 300K. Some results are
below:
Energy Average RMSD Fluct. Drift Tot-Drift
-
> Unless the box was equilibrated at NPT at the start of the NPT run, or the
> run was very long, the average value over the whole run is not all that
> likely to be one from the equilibrium range. Take the last frame.
The system is pretty equilibrated. Just look at the energy drift - it
is neglig
| email: vvcha...@gmail.com
Rochester, NY 14627-0216 | email: cha...@univer.kharkov.ua
United States of America | WWW:
chem.rochester.edu/~prezhdo_group/index.php/members/5-vitaly-chaban
> I am trying to solvate a protein in a box of acetonitrile using genbox. My
> initial s
Phys,104, 477 but thanks for your tips.
>
> Diana
>
> On Fri, 5 Nov 2010 12:59:51 -0400, Vitaly Chaban
> wrote:
>> Hey, Diana -
>>
>> I believe these acetonitrile holes are not a problem. Just perform an
>> equilibration run in the NPT ensemble and they will d
. Chaban
> Am 05.11.2010 19:16, schrieb Vitaly Chaban:
>>
>> Diana -
>>
>> I just wonder how the density of your system behaves while you run NPT
>> equilibration? Do you monitor it? Did you estimate the size of these
>> holes? Maybe they are just due
She uses "trjconv -pbc atom", so it looks like the answer is no.
On Fri, Nov 5, 2010 at 6:10 PM, Tsjerk Wassenaar wrote:
> Hey,
>
> Do the holes match the parts of the protein sticking out on the other side?
>
> Tsjerk
>
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.
Holes... Holes... What is the size of these holes? Use g_density,
g_rdf, make plots, observe peaks...
> Hi Diana,
>
> Yeah, my reply was a bit off, as Vitaly had already pointed out. Lazy
> reading, sorry. But are these holes created by genbox, or are they already
> present in the acn solven box
ith a poorly equilibrated system.
Vitaly Chaban, Ph.D.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscri
Did you try to re-run your trajectory? Does the problem persist then?
> I have a trajectory with 2 frames.
> i want to separate just 1000 last frames of it in pdb formt and 1000 first
> frames too.
> I entered this command:
> trjconv -f mmm.trr -o nnn.pdb -s lll.tpr -b 800 -e 1000
>
>
Hey, Olga -
> Also please can you tell me where can I get "ffgmx.itp" file?
/$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other
standard topology files are there.
By trying to run md I am getting an error: Fatal error:
> moleculetype UNK is redefined
Please post you top and itp fi
ation)... but it should be another keyword to control such
trick.
--
Dr. Vitaly Chaban
University of Rochester
> Indeed, the source of the problems comes from both the constraints and
> the pressure bath. The temperature bath did not seem to interfere.
>
> Now, the problem is clear, to r
>
> ;
> ; File 'creatine.top' was generated
> ; By user: onbekend (0)
> ; On host: onbekend
> ; At date: Mon Nov 15 13:24:44 2010
> ;
> ; This is your topology file
> ; it was generated using program:
> ; pdb2gmx - version 4.5-beta2
> ;
tem dynamics on
the YOUTUBE for us to look at.
> 3) temprature keeps on rising as the simulation proceeds is this all right?
No. For how much does it increase?
--
Dr. Vitaly Chaban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pleas
sure. I believe it is
>> principally impossible in spite of the force field parameters that can
>> be used. You may want to upload the video with the system dynamics on
>> the YOUTUBE for us to look at.
>>
>>
>>> 3
used (MDP file)
for the LJ interactions. I believe the problem is someplace around
this point.
--
Dr. Vitaly Chaban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
Also, as far as I understand, before NVE simulation, one should
equilibrate the system in the NVT ensemble (at the desired T) and
only then switch off T-coupling (=NVE).
Vitaly Chaban
>>> I would not say that you tube rotates so vigorously to be
>>> suspicious... The tube
> Hi, everyone
>
> I find that i used T and P coupling in water-air interface, that is the
> reason my system imploded.
>
> So i changed to NVT. But there are still fatal errors.
>
> I have some questions concerning .gro file.
>
> for example in spc216.gro, there are both + and - psotions. But in
Hi all,
What is the standard designation (if any exists) of the function that
is calculated using "g_rdf -cn"? Cumulative numbers? Running
coordination numbers? Which of them is better to be used in the
article?
Thanks for your insights.
Vitaly
Dr. Vitaly V. Chaban| skype: vvchaba
> Subject: [gmx-users] MOPAC gromacs mdreun error (vidhya sankar)
> To: gmx-users@gromacs.org
> Message-ID: <665887.73042...@web95501.mail.in.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Gerrit sir,
> Thank you for your atonce reply
> my mopac stand alone binar
Hey, Shiyong -
I believe your problem is related to X2TOP usage rather than to a
proper force field choice. I'd suggest to start with looking into N2T
files for the below entries.
Cheers.
--
Dr. Vitaly V. Chaban
Rochester, U.S.A.
> I just tried G53a6 for protein-RNA simulation. But fatal erro
Hey, Greg -
I believe the problem is more probably located in your GRO file or TOP
file rather than in MDP one. Just visualize your structure to check if
everything is OK. Also, 50 000 steps can be not enough to get the
well-equilibrated configuration. What force and energy is output at
the last s
> From: gromacs
> Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not high
> Hi,
>
> I want to simulate 3x3x0.8 water film (bulk water) first creat the water,
>
> genbox -cs -o film.gro -box 3 3 0.8
>
> then, i EM the bulk water;
>
> Using steep, but
>
> t = 0.011 ps: Water molecule
>>Hey, gromacs -
>>
>>Nice to hear from you here... It is a bad idea to simulate something
>>with any cartesian dimension lower than a couple of nanometers using
>>classical FFs. All your problems are generated by 0.8 nm of the
>>z-side.
>>
>>--
>>Dr. Vitaly V. Chaban
>>Rochester, U.S.A.
>>
>
> Th
ive an answer to all.
> At 2010-12-17 09:51:57，"Vitaly Chaban" wrote:
>>>>Hey, gromacs -
>>>>
>>>>Nice to hear from you here... It is a bad idea to simulate something
>>>>with any cartesian dimension lower than a couple of nano
gt;
>
>
> I
>
>
>
> At 2010-12-17 13:12:43，"Vitaly Chaban" wrote:
>
>>I still do not understand what physical system you want to create in
>>the MD system or what phenomenon you want to reproduce.
>>
>>If you need a water film, then the only s
the first steps.
Good luck.
Dr. Vitaly V. Chaban
On Fri, Dec 17, 2010 at 12:46 AM, Vitaly Chaban wrote:
> You SHOULD bring water to EQUILIBRIUM starting from 3x3x9 box with
> water at the center of this box. You will NEVER get EQUILIBRIUM water
> film using 3x3x0.8.
>
>
>
>
> Hi, everyone
>
> I have run the 3x3x0.8 water film in 3x3x9 box successful.
It is a time for me to proudly ask: "Was i right before?" ...
> However, I'd like to add polarization to my water model. Because if i want to
> investigate solution interface, the ordinary water model cannot reproduc
Hey -
I need to see"rrg.itp" and "drg.itp" to undesrtand the situation.
=
* Dr. Vitaly V. Chaban | skype: vvchaban *
* Department of Chemistry | email: v.cha...@rochester.edu
>
> On Sun, Dec 26, 2010 at 12:28 AM, sreelakshmi ramesh <
> sree.laks...@research.iiit.ac.in> wrote:
>
>> Dear users,
>> I did nvt equil and after that npt equilbriation and i am
>> using parinello rahman as the barostat but the prob is even after 200 ps of
>> equil the avg pressu
Hi all,
Is there a trick to analyze the temperatures of the atom groups if
they are not coupled separately? E.g. when the whole system is
T-coupled as the only group, can one determine the temperature
evolution for its parts?
Thank You.
=
Dr. Vitaly V. Chaban, Ph.D.
Depar
> while using grompp I got a message :
>
> " System has non-zero total charge: -9.98e-01"
>
> This is non integral charges. What should I add using genion?
> +1 charge? Why am I getting such non integral charges?
> I also checked for any breakage in the chain and found no such
> ends.
>
> Kindl
On Mon, Jan 17, 2011 at 9:28 AM, Justin A. Lemkul wrote:
>
>
> Vitaly Chaban wrote:
>>>
>>> while using grompp I got a message :
>>>
>>> " System has non-zero total charge: -9.98e-01"
>>>
>>> This is non integral char
Hey Gyorgy,
Your current topology file(s) is(are) also important to analyze the
situation and fix the problem.
Pass my kind regards to Julia...
Dr. Vitaly V. Chaban, Ph.D.
Department of Chemistry
University of Rochester
Rochester, New York 14627-0216
The United States o
> I am trying to calculate the Velocity Autocorrelation Function for my
> system using g_velacc. I have system of 128 ionic liquids (128 cations and
> 128 anions). I run the trajectory for 20 ns. I used following command
> g_velacc -f 3.trr -n emi-etso4-127-no.ndx -s 3.tpr -o
>
> I selected "syste
> If I want to include more than 1000 TIP4P or TIP5P water molecules in
> my MD system, how could I construct the TIP4P.gro and TIP5P.gro files
> ?
genconf -f onewater.gro -o box.gro -nbox N N N,
where onewater.gro contains the coordinates of one water molecule and
N - is a number of water molecu
> Hi
> how many water molecules used to run MD?
>
> what is the criteria for this?
So many to make your short-range potential saturated.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +
> Could anyone tell me how to construct the solvent box of TIP4P and TIP5P
> model?
First of all you should make the coordinates of one particle of the
desired model in .gro file format. For the next commands see my previous
messages.
Cheers.
--
Vitaly V. Chaban
School of Chemistry
National
o.
In fluids, this value is from 1.0 nm to 1.4 nm, for water it's even less.
See force field specifications for the exact models you use.
CYL> What is the short-range potential?
CYL> Also, how to measure the short-range potential?
CYL> Thank you
CYL> Lin
CYL> On 9/22/08, Vitaly
Jochen,
Thank you very much! I will just try it.
Vitaly
JH> Vitaly Chaban wrote:
>> Hello,
>>
>> In gromacs analysis tools, is it possible to output multiple data
>> columns as several 'parallel' columns (not as pairs delimited by '&')?
J
> What compiler should I use on Windows?
> Thank you in advance.
If you succeed it would be great if you share the resulting
binaries in the internet!
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvc
> I want to print out the complete force field paramters which the command
> "#include "ffXXX.itp" assigned.
Goto /usr/local/gromacs/share/gromacs/top/ on your system.
If the parameters mentioned in ffXXX.itp are redefined in your .top
you get a warning by grompp.
--
Vitaly V. Chaban
School of
> How does this command automatically assign the force field
> parameters which I did not assign in my .top file?
It inserts the content of ffXXX.itp into .top file.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROT
Hi Andy,
> I create a small group of atoms close to each other, say
> 10-12 atoms, the temperature of these atoms varies alot while the
> temperature the whole system does not, why is this?
A mob is always uniform. :) You have a normal situation indeed.
> Is there a way to
> accurately determin
> I heard that it takes very long to see a micelle forming.
I believe it's quite true.
> How long should be the simulation time to see the micelle forming?
> How many nanoseconds to put on the simulation?
I suggest you to use ngmx (or VMD) to monitor the trajectory and catch
the moment you are i
> how do I remove Gromacs 3.1.3? Naturally, I have the O.S. linux fedora.
> Thank you.
Delete it by hand.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698
> with hydrogen atom of other water molecule in opposite part.
It is a normal behaviour of VMD.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698
___
> Just wanted to know if GROMACS 3.3.3 supports multi threading that is can
> run four instances of mdrun in the same machine which has 4 cores...
It seems so. If I'm wrong please anybody correct me.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 6
> I am having general doubts regaring GROMACS those are unclear me writing you
> 1. If a system contain equal number of atoms run these systems in GROMACS
> and in AMBER why former one simulates faster
> than second one?
Because GROMACS is a great software.
> 2.If do minisation while running sh
>>Because GROMACS is a great software.
> Thanks for the reply, what may be the reason GROMACS became great?
Please see the tutorial as for algorithms for non-bonded interactions
in gromacs.
>> > 2.If do minisation while running shows that
>> > Back Off! I just backed up step53.pdb what may be
> Then, I can say my system is under the water model-TIP4P-Ew.
> And, other simulation procedures are all the same for any kind of water
> model.
What procedures do you mean?
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMA
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