[gmx-users] Re: how to calculate g_sdf and ionic conductivity
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Oct 21 11:32:53 CEST 2009
Hi IMA,
Have you checked the g_sdf help? It provides information about the
purpose of the four groups, and how they should be related. What
you're trying to do here is nonsensical. Do you know what you want to
do (physicochemically)?
Cheers,
Tsjerk
On Wed, Oct 21, 2009 at 11:15 AM, naimah haron naimah
<cimot_ima98 at yahoo.com> wrote:
> Dear Mark....
> Thanks for your suggestions.
> 1) Regarding to the g_sdf, the problem is I have 3 groups ( system, cation,
> anion) in my index file.
> But, before using g_sdf, I should have 4 groups. So, how about the last
> group?
> 2) When I used g_sdf command ( g_sdf -s topol.tpr -f trj.trr -n index.ndx
> -r), it mention to select the group for 4 times. My question is, how to
> select the group?
>
> THANKS
> IMA
>
> ________________________________
> From: "gmx-users-request at gromacs.org" <gmx-users-request at gromacs.org>
> To: gmx-users at gromacs.org
> Sent: Wed, October 21, 2009 3:22:12 PM
> Subject: gmx-users Digest, Vol 66, Issue 135
>
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: Re: Chloroform (CHCl3) solvent box for G53a5 force field
> (Justin A. Lemkul)
> 2. why are the values of the LJ interaction energy negative and
> the values of the Coulomb interaction energy positive between two
> group. (Jinyao Wang)
> 3. Re: why are the values of the LJ interaction energy negative
> and the values of the Coulomb interaction energy positive between
> two group. (Mark Abraham)
> 4. Fatal error: 2 particles communicated to PME node 0 are more
> than a cell length out of the domain decomposition cell of their
> charge group (wuxiao)
> 5. Re: Fatal error: 2 particles communicated to PME node 0 are
> more than a cell length out of the domain decomposition cell of
> their charge group (Mark Abraham)
> 6. g_rdf and number of atoms to include (Enemark Soeren)
> 7. how to calculate g_sdf and ionic conductivity
> (naimah haron naimah)
> 8. Re: how to calculate g_sdf and ionic conductivity (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 20 Oct 2009 19:18:05 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5
> force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4ADE452D.6090602 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Pablo Englebienne wrote:
>
>> Thanks for confirming this, Justin.
>>
>> I decided not to use the user-contributed CHCl3 box because the topology
>> is not consistent with the GROMOS atom types: the CH is united atom
>> (although the mass is 12.01100, it should probably be 13.01900?), while
>> in G53a5 there are parameters for C, H and Cl. Has someone ever used
>> this box successfully?
>>
>> I was able to equilibrate the box in NVT (100-200ps gives a stable
>> simulation), although it exploded at constant pressure. After looking at
>> some references on the mailing lists (both GMX and AMBER), I tried
>> increasing tau_p from 2.0 to 5.0 and that yielded a stable 100 ps
>> simulation, although the system later (continuing for further ~150 ps)
>> started to oscillate wildly in temperature and pressure.
>>
>> What is the effect of increasing tau_p? Besides making the dynamics
>> stable, would changing its value affect the outcome of the simulation in
>> any other way?
>
> By increasing tau_p you are reducing the stringency of the pressure
> coupling,
> i.e. allowing the system to change a bit more between coordinate scaling.
> By
> decreasing the frequency of coordinate scaling in extremis, you would lose
> the
> benefit of pressure coupling and achieve an NVT ensemble, with the box
> dimensions being essentially static. In the case of a tau_p of 2.0 vs. 5.0,
> you
> should not have this problem.
>
> If the provided box uses a united-atom CH, I would suspect it is not
> suitable
> for GROMOS96 parameters, as you have discovered. In all G96 variants, the H
> is
> explicitly represented. You might consider coming up with your own box.
> Start
> with a coordinate file for one molecule, use genconf to generate a box, and
> equilibrate.
>
> If you want any further information about diagnosing the current problem,
> posting the .mdp file would be helpful.
>
> -Justin
>
>>
>> Thanks again!
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use thewww
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 21 Oct 2009 10:18:19 +0800
> From: "Jinyao Wang" <wangjy at ciac.jl.cn>
> Subject: [gmx-users] why are the values of the LJ interaction energy
> negative and the values of the Coulomb interaction energy positive
> between two group.
> To: "gmx-users" <gmx-users at gromacs.org>
> Message-ID: <456090806.02727 at ciac.jl.cn>
> Content-Type: text/plain; charset="gb2312"
>
> Hi gmx-users,
> I have calculated the interaction energy between two group. But I find
> that the values of the LJ interaction energy are negative and the values of
> the Coulomb interaction energy are positive between two group. So I think
> the LJ interaction is attractive and the Coulomb interaction is repulsive.
> Is it correct for my consideration of the interaction ?
>
>
>
>
>
> Jinyao Wang
> wangjy at ciac.jl.cn
> 2009-10-21
>
> ------------------------------
>
> Message: 3
> Date: Wed, 21 Oct 2009 13:26:22 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] why are the values of the LJ interaction
> energy negative and the values of the Coulomb interaction energy
> positive between two group.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4ADE714E.5000704 at anu.edu.au>
> Content-Type: text/plain; charset=GB2312
>
> Jinyao Wang wrote:
>> Hi gmx-users,
>> I have calculated the interaction energy between two group. But I find
>> that the values of the LJ interaction energy are negative and the values of
>> the Coulomb interaction energy are positive between two group. So I think
>> the LJ interaction is attractive and the Coulomb interaction is repulsive.
>> Is it correct for my consideration of the interaction ?
>
> Maybe. That conclusion would assume
> a) that you've calculated it correctly,
> b) that the model physics is robust with respect to such a decomposition
> when it almost certainly wasn't parameterized for such a property, and
> c) the decomposed interaction energy means anything.
>
> Mark
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 21 Oct 2009 10:31:49 +0800
> From: wuxiao <xiaowu759 at hotmail.com>
> Subject: [gmx-users] Fatal error: 2 particles communicated to PME node
> 0 are more than a cell length out of the domain decomposition cell of
> their charge group
> To: <gmx-users at gromacs.org>
> Message-ID: <BAY131-W17839D5AC63D6A98F4E4ECE9BF0 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
>
>
> Dear GMXers,
>
> When I perfomed a MD simulation, it always teminated after about 700 ps
> with the message:
>
> Fatal error: 2 particles communicated to PME node 0 are more than a cell
> length out of the domain decomposition cell of their charge group
>
> I utilized the GROMACS-4.0.5. I have searched the maillist to find some
> similar posts but they can not yet cope with this issues. Could you give me
> some clues, please?
>
> Best wishes,
>
> Chaofu Wu, Dr.
>
> _________________________________________________________________
> Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！
> http://im.live.cn/safe/
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20091021/c8985b2e/attachment-0001.html
>
> ------------------------------
>
> Message: 5
> Date: Wed, 21 Oct 2009 13:58:24 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Fatal error: 2 particles communicated to PME
> node 0 are more than a cell length out of the domain decomposition
> cell of their charge group
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4ADE78D0.2000304 at anu.edu.au>
> Content-Type: text/plain; charset=GB2312
>
> wuxiao wrote:
>> Dear GMXers,
>> When I perfomed a MD simulation, it always teminated after about 700
>> ps with the message:
>> /Fatal error: 2 particles communicated to PME node 0 are more than a
>> cell length out of the domain decomposition cell of their charge group/
>> I utilized the GROMACS-4.0.5. I have searched the maillist to find
>> some similar posts but they can not yet cope with this issues. Could you
>> give me some clues, please?
>
> Yep. http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> Mark
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 21 Oct 2009 13:28:39 +0800
> From: "Enemark Soeren" <chees at nus.edu.sg>
> Subject: [gmx-users] g_rdf and number of atoms to include
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <C178399C57FF284FA0022B75E348721905E7A9BF at MBX03.stf.nus.edu.sg>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear users,
>
>
>
> I would like to compare interactions between molecules by using RDF. I
> have tried looking at glycine and water, and compare the following two
> interactions:
>
> 1) between the amine hydrogen atoms in glycine and the oxygen atom
> in water
>
> 2) between the carboxyl oxygen atoms in glycine and the oxygen atom
> in water
>
>
>
> However, my result in 1) depends on how many of the 3 hydrogen atoms I
> include in the calculations. Why is that? Does that mean that I cannot
> directly compare the strengths (RDF peak height) of the two interactions
> as they are not based on the same number of atoms? Does it also mean
> that I must always calculate RDFs by using 1 atom on each of the
> particles/groups that I am comparing?
>
>
>
> Thanks,
>
> Soren
>
>
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20091021/31a92441/attachment-0001.html
>
> ------------------------------
>
> Message: 7
> Date: Tue, 20 Oct 2009 23:48:12 -0700 (PDT)
> From: naimah haron naimah <cimot_ima98 at yahoo.com>
> Subject: [gmx-users] how to calculate g_sdf and ionic conductivity
> To: gromacs <gmx-users at gromacs.org>
> Message-ID: <662629.64091.qm at web36505.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello all........
>
> Did anyone know how to
> 1) calculate g_sdf?
> 2) ionic conductivity?
>
> Can I have the commands for that....
>
> Thanks
>
> IMA
>
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20091020/7469faa9/attachment-0001.html
>
> ------------------------------
>
> Message: 8
> Date: Wed, 21 Oct 2009 18:20:40 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] how to calculate g_sdf and ionic conductivity
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4ADEB648.1010308 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> naimah haron naimah wrote:
>> Hello all........
>>
>> Did anyone know how to
>> 1) calculate g_sdf?
>
> Start with g_sdf -h.
>
>> 2) ionic conductivity?
>
> Don't know. Look in manual 7.4, 8 and maybe Appendix D.
>
>> Can I have the commands for that....
>
> If you do some more of your own work and ask focussed questions you help
> yourself look worth helping :-)
>
> Mark
>
>
> ------------------------------
> Dear Mark....
> Thanks for your suggestions.
> 1) Regarding to the g_sdf, the problem is I have 3 groups ( system, cation,
> anion) in my index file.
> But, before using g_sdf, I should have 4 groups. So, how about the last
> group?
> 2) When I used g_sdf command ( g_sdf -s topol.tpr -f trj.trr -n index.ndx
> -r), it mention to select the group for 4 times. My question is, how to
> select the group?
>
> THANKS
> IMA
>
>
>
>
> _____________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 66, Issue 135
> ******************************************
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
More information about the gromacs.org_gmx-users
mailing list