If seems in the gmx versions above 4.0 '-np' is not used. If I am not
mistaken you should just point out the number of nodes in your queueing
system while submitting the job.
Vitaly
> I am trying to do my position restrained dynamic simulation on GROMACS
> 4.0.4, and I want to use 4 nodes on th
Please read about obtaining diffusion constant from VAC in the gromacs wiki.
I wrote an individual article on that topic.
Best,
Vitaly
Subject: RE: [gmx-users] transport properties
> To: Discussion list for GROMACS users
> Message-ID: <569363.99887...@web36304.mail.mud.yahoo.com>
>
nged.
> How can I really fix the atoms? Look forward
> for your suggestions!
>
All the atoms which relate to your frozen groups should be non-movable
during MD.
>the coordinates of C and O in carbonyl groups changed.
Only ones of CHO changed? And the CNT itself is nonmovable
le atoms in
> carbonyl groups take charges.
>
> Thank you for your time!
>
>
> - 原始邮件 -
> 发件人：Vitaly V. Chaban
> 收件人：gmx-us...@gromacs.org
> 主题：[gmx-users] Re: How to freeze the atoms?
> 日期：2009-6-23 18:04:35
>
> >
> > Dear all
> >
Car" and the group name of carbonyl in
>> the ndx file is "Car", too. Is there anything wrong with the groups?
>>
>> Is it possible that the frozen atoms move a short distance due to the
>> strong electrostatic forces. C in the CNT has no charge, while atoms
I used the DMSO model from dmso.itp for some test runs with the gromacs
versions before 4.0 and it gave me the same diffusion constant (~1.1) as
reported in the original paper. So, the topology seems to be OK in general.
Please also see the paper of Skaf (it seems of 1997) for DMSO force field...
I do not see topology file in your archive.
2009/6/25
> The input files for EM of the job are in the attachment.
>
>
>
> Thank you for your time!
>
>
> - 原始邮件 -
> 发件人：Vitaly V. Chaban
> 收件人：toby10222...@sina.com, gmx-users@gromacs.org
> 主题：Re: 回复：Re:
Hi,
In what units C6 constants are present in the force field files?
Thank you,
Vitaly
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Please search the archive at http://www.gromacs.org/search bef
example of them? Thanks.
>
>
The examples are in the topology folder of the gromacs installation. As for
me they are quite self-explanatory.
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@un
D for some time to relax the system completely.
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
Hi
>
>
>
> I
Hi,
Can anybody share any working code which uses xdr-1.1 library? - Just to
consult.
Thank you very much in advance,
Vitaly
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Please search the archiv
his error before adding
> ions.
>
> Can anybody help me regarding same and suggest what could be possible
> reason for this ?
>
> Thanks,
>
> Regards,
>
I guess you just missed five atoms in your gro file. Does the number of
solvent molecules in the coordinate file equal
ve this error.I am getting this error before adding
> >> ions.
> >>
> >> Can anybody help me regarding same and suggest what could be possible
> >> reason for this ?
> >>
> >> Thanks,
> >>
> >> Regards,
&
> --
> >> >>
> >> >> I checked gromacs wiki page
> >> >> also(
> >> >>
> >>
> http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_
In what way do you install this software: from source or from packages?
Do you have the appropriate variable telling the grace where the lesstiff is
installed? If you install lesstiff from the package it should have a name
like "lesstiff-dev" (not just lesstiff).
~ Vitaly
--
Vitaly
Hello Shamik,
Why not to try from rpm packages? It should be easier especially if this is
the fisrt time of doint that.
~ Vitaly
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua
V. Chaban, Ph.D. (ABD)
School of Chemistry V.N. Karazin Kharkiv National University, Svoboda sq.,4,
Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
Hi Vasya,
Glad to hear from you here! I did not work with -rerun yet - it's a useful
option I see now.
On Mon, Jul 20, 2009 at 5:39 PM, Vasilii Artyukhov wrote:
>
>
> 2009/7/20 Vitaly V. Chaban
>
>> Hi Matteus,
>>
>> Yeah, dynamic groups would be a po
senseless. The linux distribution will not affect gromacs
performance.
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-0
What about .gro files?
>
> I appreciate your help for solve my basic problems.
>
> Thanks, Jamie
>
Jamie,
Please see the help for genbox, genconf and editconf utlities of the gromacs
package. It seems you should be interested in Protein Data Bank as well:
http://www.rcsb.org/pdb/h
etc).
3. The nanotubes files (coordinates and topologies) as well as a number of
already equilibrated systems were uploaded by me to the topology section of
the old site. I guess they are still accessible. You may also want to look
for Christopher Stiles' wonderful page with many details.
when I changed the thermostat to nose-hoover, it said that it can not
> be used with Berendsen barostat. Why?
>
> C'est la vie...
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@un
Yeah, we are friendly. :)
Don't hesitate to ask if you experience future problems.
~ Vitaly
On Wed, Jul 22, 2009 at 1:55 AM, Jamie Seyed wrote:
> Thank you for your help and comments.
> -Jamie
>
>
>
>
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comes out that non-running windows interfere gromacs
run.
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.un
file
> to make sure no particles are overlapping with the original box? Or no
> particle is coming from the new one in the old one?
>
>
>
> Payman
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban
>
om
> becomes infinity. This will cause the simulation to crash!
>
>
>
> Payman
>
>
>
> *From:* Vitaly V. Chaban [mailto:vvcha...@gmail.com]
> *Sent:* July 22, 2009 2:20 AM
> *To:* Payman Pirzadeh; gmx-users@gromacs.org
> *Subject:* Re: genconf
>
>
>
>
Jamie,
To have a trajectory in TRR you should just change
>
> nstxout=0
> nstvout=0
>
>
to non-zeros.
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@
Hi,
I can't download the software form the users contributions section
located on the old gromacs website
(http://oldwww.gromacs.org/component/option,com_docman/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,35/).
As pressing "download" it seems to open binary file in the browser
wind
Thanks, Justin. I succeeded eventually with your link.
Vitaly
On Wed, Jul 29, 2009 at 11:54 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Hi,
>>
>> I can't download the software form the users contributions section
>> lo
a.n2t
>
> WARNING: all CONECT records are ignored
>
> Opening library file
> /homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.n2t
>
> There are 23 name to type translations
>
> Generating bonds from distances...
>
> atom 0
>
>
>
> ... and at this point it
ogies
> www.dti.supsi.ch
> SUPSI - University of Applied Science of Southern Switzerland
> www.supsi.ch
>
> Via Cantonale - Galleria 2
> 6928 Manno
> Switzerland
> tel: +41 (0)58 666 66 46
> fax: +41 (0)58 666 66 20
>
>
> -Messaggio originale-
> Da: Vi
icimsi.ch
> DTI - Department of Innovative Technologies
> www.dti.supsi.ch
> SUPSI - University of Applied Science of Southern Switzerland
> www.supsi.ch
>
> Via Cantonale - Galleria 2
> 6928 Manno
> Switzerland
> tel: +41 (0)58 666 66 46
> fax: +41 (0)58 666 66 20
boundary conditions for infinite molecules
> seem to be handled correctly...
>
> 2009/7/30 Vitaly V. Chaban
>>
>> Giulio,
>>
>> I suggest you to try x2top which is spread with gromacs-3.3.1. The
>> newer versions of x2top are not sain.
>>
>> Vi
rsity of Applied Science of Southern Switzerland
> www.supsi.ch
>
> Via Cantonale - Galleria 2
> 6928 Manno
> Switzerland
> tel: +41 (0)58 666 66 46
> fax: +41 (0)58 666 66 20
>
> -Messaggio originale-
> Da: Vitaly V. Chaban [mailto:vvcha...@gmail.com]
> Inviato: gio
If you unzipped/untarred the archive properly it should be some system
already prepared to run. So you can just start grompp and mdrun to
begin MD.
>
> By the way, I had already seen that web page... I downloaded and unzipped the
> swcnt file, but I can't understand what kind of file it is.
>
__
>
> Hello,
>
> I downloaded "topolbuild1_2_1.tgz" from the URL:
> http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz
>
It seems you are right. I tried the same and also found the archive broken.
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V
Hi,
Did you try pdb2gmx, x2top to make .top and then export to .itp?
Sometimes also it appears easier to make the topology by hand if your
structure is not big. Please see the topologies for some molecules in
the gromacs archive to use them as an example.
Vitaly
>
> Dear gmx users,
> I need some
tried but I got error messages for both cases.
> Actually the structure is big and contains a c60 part. Do you have any
> advice? I could not find in the topology part of archive...
> Thanks/Jamie
>
>
> On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban wrote:
>>
>> Hi,
that something
> else?? I appreciate your help...
> Thanks a lot/Jamie
>
> On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban
> wrote:
>>
>> Jamie,
>>
>> What error messages do they provide? What force fields do you use?
>> There were many rumors about the
t; 2) with Christopher Stiles method, why I got that fatal error and how I can
> solve it to run a correct md simulation??
> Many Thanks in advance/Jamie
>
> On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban
> wrote:
>>
>> Jamie,
>>
>> The best solution is
mixed the ff and I put ff.itp on the top of my topology file...
> would you please let me know what is causing the problem?? I appreciate your
> help.../Jamie
>
> On Mon, Aug 10, 2009 at 4:29 PM, Vitaly V. Chaban
> wrote:
>>
>> Dear Jamie,
>>
>> > 1) when I h
t;> the case I am going to undo it to see what happens... I will let you know.
>> Thanks/Jamie
>> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban
>> wrote:
>>>
>>> Why did you comment out [defaults] in ffoplsaa.itp? The general idea
>>> is that the
nclude "c80ch3.itp"
> [system]
> fullerene in water
> [molecules]
> C80CH3 1
> SOL 1000
>
> my command is:
> grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr -maxwarn 10
>
> Thank you for helping me out to solve the problem/ Regard
system is a polymer
> (dendrimer) without pbc. I wonder if this is a bug for MPI of GROMACS. Could
> you give me some hints? Thanks a lot for your attention!
>
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Uk
&step_xtc, &time_xtc, box_xtc,
> x_xtc, &prec_xtc);
> printf("%f %f %f\n",x_xtc[0],x_xtc[1],x_xtc[2]);
>
> The coordinates in the variable x_xtc seems to be random. How do I access
> the proper coordinates from the trajectory?
>
> I would appreciate any help.
than me can provide such one, I will be very
grateful.
Thanks,
Vitaly
-- Forwarded message --
From: Vitaly V. Chaban
Date: Tue, Aug 11, 2009 at 11:11 PM
Subject: Re: xdrfile library, read co-ordinates from .xtc
To: gmx-users@gromacs.org, Lipi Thukral
Hi Lipi,
What do you
Janne, Jussi,
Thank you very much!
Vitaly
On Wed, Aug 12, 2009 at 11:35 AM, Janne Blomqvist wrote:
> Vitaly V. Chaban wrote:
>>
>> On the same topic, I have a question to the community: does anybody
>> try to make *so*-library (or *dll* on windows) of xdrfile in order
Jamie,
I didn't understand why you meant saying "waters far from the outside
of the pore"... Far from outside, then where exactly? Maybe I just
imagine your box incorrectly.
To fill the pore with a solvent try to "deceive" genbox a little:
1) make a box (see editconf) in such a way that it contai
> first without introducing my molecule...
> I appreciate to get more information and some help... Thanks a lot/Jamie
>
>
> On Thu, Aug 13, 2009 at 12:21 PM, Vitaly V. Chaban
> wrote:
>>
>> Jamie,
>>
>> I didn't understand why you meant saying &quo
Fatal error:
> One of the box vectors has become shorter than twice the
> cut-off length or box_yy-|box_zy| or box_zz has become smaller than the
> cut-off.
> ---
> Thanks in advance/Jamie
>
>
> On Thu, Aug 13, 2009 at 2:10 PM, Vitaly
Tsjerk,
I understood the situation in such a way that MD was not run at all,
so Jamie visualizes *gro* file obtained with *genbox*...
Jamie,
didn't you look at this: http://www.ime.unicamp.br/~martinez/packmol/
to prepare your system?
Vitaly
>
>> Thanks for the answer. When I said far away me
Hi,
1. It seems you also need to include xdrfile.h.
2. Are the library files located in the same directory with your
source files when you link?
VItaly
>
> Recently I am trying to use the xdr library downloaded from gromacs org to
> read xtc files. However when I link my program with the library
Hi all,
In what way is gromacs list digest actually formed? How the system
decides that the time to form and send the list digest comes?
During the last days I got many digests (more than 5 ones a day) many
of which contained only 1 or 2 messages, that seems quite
inconvenient. Maybe it's reasona
Jamie,
How do you like g_vellacc or g_dipoles? :)
Best,
Vitaly
>
> Dear all,
> Is there any tool in gromacs that can calculate time correlation
> function ??? R(x,y,z). Many Thanks in Advance/Jamie
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---
> Program grompp, VERSION 4.0.4
> Source code file: topio.c, line: 415
>
> Fatal error:
> Syntax error - File topol.top, line 4
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
>
r shows that
> the job is running, also the processors are 100% engaged while I have no
> outputs!
A standard guess: what about trying to run the single-processor job on
the same cluster? Does it run OK?
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National Univer
aymon Pirzadeh wrote:
> Yes,
> it works when it is run on one processor interactively!
>
> On Thu, 2009-08-27 at 09:23 +0300, Vitaly V. Chaban wrote:
>> > I made a .tpr file for my md run without any problems (using the bottom
>> > mdp file). My job submission scrip
Hi George,
I know some attempts of gold nanosize particles simulation published
during the last years. Did you explore the literature?
~ Vitaly
>
> Hi GROMACS users
>
> Does anyone have any information on the simulation of gold nanoparticles with
> GROMACS?
>
> Thank you in advance
>
> George
_
> Do you have any suggestions on what options to use in the configure command
> when installing GROMACS for parallel run? Is it possible to change these
> options at a later time?
>
> Thank you in advance
>
> George
I suppose "--enable-mpi" will be enough to make
Hi,
Your objects look very familiar for me. :)
One can't make .gro from .itp. You should first make .pdb with
coordinates. By the way gromacs works with .pdb directly.
Good luck,
Vitaly
> Thanks a lot for your reply. Actually I will tell you the
> problem. I want a binary mixt
So what's your goal? If you have .pdb of one molecule, it's easy to
disseminate it using genconf or genbox.
On Tue, Sep 1, 2009 at 3:49 PM, Abhishek Banerjee wrote:
> hi,
> Actually I checked what you told me to do. I used genbox -ci DMF.pdb
> -box 10 10 10 -nmol 100. Then I am getting a ra
Banerjee,
I understand your task but I still did not understand your problem on
this way. First you should have the .pdb with methanol molecule
(coordinates) and the .pdb with DMF (coordinates). Then use genconf or
genbox to make a box of pure methanol (or DMF) and add another species
with genbox.
It seems gromacs can be compiled on windows directly if you a bit lucky.
And what's the sense of this task? Do you have a cluster running windows?
Vitaly
> Hi all
>
> I would like to ask if it is possible to use MPI when GROMACS is installed on
> Windows using Cygwin. If yes, is there any spec
fied and no makefile found. Stop."
>
> What should i do for this? Should i save the GROMACS Directory somewhere
> else?
>
>
Hi,
What does your configure script finish with?
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National Univer
automatically. The second
way is to make topology by hand. If one has enough experience it can be of
some pleasure. :)
Good luck!
Vitaly
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha
rst question
is: what charge (integer) of the system do you expect? May the value
you report here occur due to the wrong force field you apply?
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@unive
In a word, do you use a respectable FF or a instantly made one? :)
~ Vitaly
On Sun, Sep 13, 2009 at 11:06 AM, Tsjerk Wassenaar wrote:
> Hi,
>
> On Sun, Sep 13, 2009 at 8:55 AM, Vitaly V. Chaban wrote:
>>> before energy minimization step , I performed the preprosessing step
yntax.
Thanks a lot!
Vitaly
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, cell.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban
Hi,
Could anybody please suggest me what is the syntax of N2T files? The
only sentence I found in the manual tells that it is "atom to atomtype
translation table". What do the numbers mean?
Thanks,
Vitaly
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Hi,
I which file should one look for the value of shear viscosity as using
"g_energy -vis" to calculate it?
Thanks,
Vitaly
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Please search the archive
Hi,
I have got confused with setting up improper dihedrals in the gromacs
topologies. In the manual (ver. 4.0) I see the section named [
impropers ] (page 104)
"
[ impropers ]
C O1 O2 CA
"
but in the example system of the peptide
(share/gromacs/tutor/speptide) one finds defining impropers using t
Justin,
It looks especially strange for me that all these files contain only
the columns of data
but not the resulting shear viscosity value.
Vitaly
On Tue, Sep 22, 2009 at 8:26 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Hi,
>>
>> I which f
l.top:
[ dihedrals ]
atoms func angle constant
1 2 6 7 2180 4.602
Will this line do what I want here?
Vitaly
On Wed, Sep 23, 2009 at 1:53 PM, Vitaly V. Chaban wrote:
> Hi,
>
> I have got confused with setting up improper dihedrals in the gromacs
> topologies. In the ma
Justin,
I think force field specific syntax is important for the utilities
like pdb2gmx or x2top but not for grompp which works with topol.top.
Here, I do not use any "standard" force field but define everything
myself from the very beginning. I believe this format (in topol.top)
should be FF-inde
Hi,
When using g_energy to calculate viscosity ("g_energy -vis"), in
enecorr.xvg the ACF of stress tensor is output. How can one specify
the "acflen" of this ACF?
I try the key "g_energy -vis -acflen XXX" but the length of the ACF is
still equal to the half of the trajectory length.
Thanks,
Vital
Hi,
Is it possible in gromacs to make 1-4 interaction energy reduced as
compared to the intermolecular interations between the same centers?
In other words, I want the INTRAmolecular interaction A-B to be by
some factor smaller than INTERmolecular A-B interactions in the box.
Thanks,
Vitaly
_
Mark,
In "g_energy -h" I see nothing abous viscosity except the option
"-vis". The command line is as I wrote earlier:
"g_energy -vis -acflen 1001"
The system is liquid water. The simulation time is 2 000 ps. The file
I look into is enecorr.xvg.
What the error of some sort do you mean?
Vitaly
> Viscosity in g_energy is computed from the pressure tensor which is
> stored in the energy file. Unfortunately is seems like the acflen is
> ignored in this case. Please submit a bugzilla.
Done.
> On the other hand you need all the data you can get for this quantity,
If the system is very big
> Viscosity in g_energy is computed from the pressure tensor which is
> stored in the energy file. Unfortunately is seems like the acflen is
> ignored in this case. Please submit a bugzilla.
Done.
> On the other hand you need all the data you can get for this quantity,
> because it converges extr
Hi,
editconf -f waters.pdb -o conf.pdb
As for CHARMM, you may select the atoms of interest and incorporate to
your topology (see chapter 5 of the manual)
Also maybe some script for the conversion exist, try to search.
Vitaly
>
> Hello everyone,
> Thanks to Justin Lemkul and Thomas Schlesier fo
Hi Simone,
I would advise you to insert the needed number of waters (genbox -cp
conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO
((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just
equilibrate.
Vitaly
>
> I need to run a simulation of a protein in a water/DMSO mixtur
Justin,
Simeone will insert only "the needed number of waters" but not the
full box. :) To do so he will use an option "-maxsol XXX" of genbox.
Vitaly
On Mon, Sep 28, 2009 at 5:08 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Hi Simon
> Viscosity in g_energy is computed from the pressure tensor which is
> stored in the energy file. Unfortunately is seems like the acflen is
> ignored in this case. Please submit a bugzilla.
>
> On the other hand you need all the data you can get for this quantity,
> because it converges extremely
If your model gives a correct fluid density with NPT, use NPT. If it
does not, then use NVT.
This is a quick practical guide, not not read much. :)
Vitaly
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> Vitaly V. Chaban wrote:
>> If your model gives a correct fluid density with NPT, use NPT. If it
>> does not, then use NVT.
>> This is a quick practical guide, not not read much. :)
>
> Sounds dangerous :-) If the model produces a wrong density, you'd want
&
would advise to start with X2TOP and CHAPTER 5 of the manual.
Vitaly
--
Vitaly V. Chaban, Ph.D.
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, cell.: +38-097-825
--
Vitaly V. Chaban, Ph.D.
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, cell.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
!
> Dear users,
>
> How is it possible to fix the number of solvent molecules and the size of the
> box used so that I can maintain exactly the same environment for different
> runs.
> For eg, if I have 84000 water solvent molecules and the dimensions of 6.7
> 6.73 4.71 nm; how can I use the same
Hi all,
I am trying to master the art of shear viscosity calculation using
"g_energy -vis". Plotting the first column in visco.xvg over time, the
nearly straight line is obtained. Is it OK? How can one get the
viscosity value from these data? My simulation details for this task
are: NVT, 298K, shi
On Thu, Oct 29, 2009 at 1:14 PM, David van der Spoel
wrote:
> Vitaly V. Chaban wrote:
>>
>> Hi,
>>
>> Is there any place to read how gromacs treats polarizable models?
>> The only thing I found in the official manual is that shells are
>> denoted as
And one more question: is this the only "polarizability scheme"
currently incorporated in gromacs? Is there any place to read about it
except the source code?
On Thu, Oct 29, 2009 at 1:14 PM, David van der Spoel
wrote:
> Vitaly V. Chaban wrote:
>>
>> Hi,
>>
&g
Hi,
The easiest way to fix the problem is to decrease the current
timestep. Also please read about -dd and -rdd keys of mdrun utility.
Vitaly
> One of my simulations just crashed after 660,000 steps with the
> following message:
>
> Step 660560:
> The charge group starting at atom 4100 moved th
I think the problem is hidden in your water force field model.
> The simulation system is merely water + one lysozyme.
> I increase temperate to 550K.
>
> Then, the simulation broke.
> The following message is shown.
>
> MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0)
> m
> Vitaly V. Chaban wrote:
>> I think the problem is hidden in your water force field model.
>
> On what basis? The user hasn't provided any information to suggest it's
> other than a poorly-conditioned integration.
On the basis of intuition. Most of the known water
The selection of FF depends on what you study. Perhaps, none of them
will be useful for you. The existing ones differ at least by the
procedures if generation although many parameters are very close.
>
> What are the main differences between the force fields used in gromacs? In
> which scenarios
Hi,
Please let me know which of the gromacs utilities is responsible for
heat of vaporization calculation.
Thanks in advance,
Vitaly
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Please search the archive at http://www.gromacs.org/search b
Hi,
Please suggest why is the reason that 1-4 term is not displayed (to be
selected for calculation) in the g_energy utility? I have two kinds of
objects (with 25 and 5 atoms) in my system - with "nexcl" equal to 3
and 2. I guess the 1-4 term may not be displayed if there is no 1-4
interactions bu
>> Hi,
>>
>> Please suggest why is the reason that 1-4 term is not displayed (to be
>> selected for calculation) in the g_energy utility? I have two kinds of
>> objects (with 25 and 5 atoms) in my system - with "nexcl" equal to 3
>> and 2. I guess the 1-4 term may not be displayed if there is no 1-
Hi,
Is there a way to output only intramolecular interaction (LJ and
Coulomb but not bond, angle, etc) energies (with a respect of
exclusions, of course). It seems LJ-(SR) and Coulomb-(SR) terms in
g_energy include all interaction, both inter- and intramolecular ones.
Thanks,
Vitaly
--
gmx-users
On Sat, Dec 5, 2009 at 10:40 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Hi,
>>
>> Is there a way to output only intramolecular interaction (LJ and
>> Coulomb but not bond, angle, etc) energies (with a respect of
>> exclusions,
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