[gmx-users] Re: gmx-users Digest, Vol 81, Issue 204
Thomas Koller
koller-thomas at gmx.de
Sat Jan 29 08:32:22 CET 2011
Hello!
Due to the fact that I still got no reply I ask you once more:
i) I studied the topic of autocorrelation function in Gromacs. For instance, I can define any distance between different atoms of my molecule over time (g_dist) as *.xvg file. For g_analyze, I use this as input and plot the autocorrelation function (-av) and can fit it with -fitfn exp. But when I want to use the Legendre option -P 2 to get a second order legendre polynomial (which is used quite often in literature) the error appears:
Incompatible mode bits: normal and vector (or Legendre)
I think that I need vectors but this can not be done in Gromacs, does it?. How can I get Legendre functions, also for dihedrals?
ii) I use bond type 1 (harmonic bond potential), but I get always linear spiky bond distribution functions, no Gaussian distribution. What is the problem?
I'm looking forward to your answers! Thanks.
Thomas
-------- Original-Nachricht --------
> Datum: Wed, 26 Jan 2011 14:46:57 +0100 (CET)
> Von: gmx-users-request at gromacs.org
> An: gmx-users at gromacs.org
> Betreff: gmx-users Digest, Vol 81, Issue 204
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> Today's Topics:
>
> 1. Re: validation of ligand parametrization (mohsen ramezanpour)
> 2. decorrelation function (Thomas Koller)
> 3. Re: Re: segmentation fault while running eneconv (Anna Marabotti)
> 4. Re: Re: Re: segmentation fault while running eneconv
> (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 26 Jan 2011 16:05:44 +0330
> From: mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
> Subject: Re: [gmx-users] validation of ligand parametrization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTinPe-vGEnzsQ_wPciYSTU1-xB549qigBhcKQ0+y at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Dr Mark
> Thanks for your guidances.
> I am sorry for my last question.My english is not very good,I hope I could
> say what was in my mind not what you read :-)
> by the way,Thanks for your attention and your reply.
>
> On Wed, Jan 26, 2011 at 3:55 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au>wrote:
>
> > On 26/01/2011 11:10 PM, mohsen ramezanpour wrote:
> >
> > Dear Justin
> > I don't want to rely on PRODRG server as others.
> > I want to do my work as accurate as possible.
> > Absolutely I read your papar and I know PRODRG present bad results for
> > estimating free energies.
> > I want to parametrize my drugs by GROMOS43A1 parameters as you said.
> > I know completely how to do it.Thanks for your and other user's
> guidances.
> > Actually I couldn't find any experimentally data to try to obtain it's
> > result.Then i have to
> > do what you said.(re-evaluating force field choice and .....)
> >
> >
> > Sounds wise.
> >
> >
> > Can you please say me more about this method?
> >
> >
> > It sounds to me like he's said plenty of useful things on the topic :-)
> A
> > question with a precise focus is much more likely to attract somebody's
> > interest. Otherwise, it can sound too much like you're asking for your
> work
> > to be done for you!
> >
> > Back on point, if you can't determine a basis for the kind of empiricism
> > GROMOS forcefields require, then you may want to choose one of the other
> > force fields with a more automated method. That doesn't remove the need
> to
> > validate, or the conundrum if validation fails, however. It's very easy
> to
> > do a worthless simulation. Many of them are. Many more of them become so
> > because they don't describe enough detail that they could be reproduced.
> For
> > example, lots of people say just "I used PME with x cutoff" in the same
> way
> > they did in the 1990s when they used a plain cutoff. I've read three
> such in
> > the last week. However, that statement is almost useless as an indicator
> of
> > quality in the electrostatic model. (Oops, I've digressed. Oh well.)
> >
> > Mark
> >
> >
> > Did you have something like this in your papers?
> > Thanks in advance for your reply
> >
> > On Wed, Jan 26, 2011 at 3:14 PM, Justin A. Lemkul <jalemkul at vt.edu>
> wrote:
> >
> >>
> >>
> >> mohsen ramezanpour wrote:
> >>
> >>> Dear All and specially Dear Dr.Justin
> >>> I generated parameters for a typical ligand.
> >>> now I want to validate it.
> >>> How can I do it?
> >>> Please let me know references for doing this.
> >>> Of course I have read the article by Dr.Justin(Alzeimer),Unfortunately
> I
> >>> couldn't understand it completely and very good.
> >>>
> >>
> >> I will assume that you're still using one of the Gromos force fields
> for
> >> your work. Gromos parameterization relies on reproduction of
> >> condensed-phase behavior, in theory, the partitioning of the species of
> >> interest between hydrophobic and aqueous media. Ideally, you would
> >> calculate deltaG of hydration in different media, but such information
> is
> >> not always readily available. That's why I turned to an alternate
> approach
> >> in the paper you mention, but one that holds in the same spirit of the
> force
> >> field and for which I had experimental evidence with which to compare.
> >>
> >> If you don't have any suitable experimental data regarding your ligand,
> >> you should re-evaluate your force field choice and consider whether or
> not
> >> parameterizing a bunch of unknown compounds is a viable approach.
> >>
> >> I certainly cannot help you better if you simply say you don't
> understand
> >> something. What isn't clear?
> >>
> >>
> >> Is there any other article who has done validation after
> parametrization?
> >>>
> >>
> >> Some, but (unfortunately) not many. Numerous authors seem to blindly
> >> rely on PRODRG, which was the motivation behind our most recent work
> (in
> >> JCIM, which I believe you said you've read). See the references
> therein for
> >> a few examples of attempts that have been made to derive and validate
> proper
> >> parameters. More rigorous standards are really necessary to avoid
> potential
> >> inaccuracies in these types of simulations.
> >>
> >> -Justin
> >>
> >>
> >> Thanks in advance for your guidance.
> >>>
> >>>
> >>
> >> --
> >> ========================================
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> ========================================
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
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> >
> >
> >
> > --
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> ------------------------------
>
> Message: 2
> Date: Wed, 26 Jan 2011 13:38:57 +0100
> From: "Thomas Koller" <koller-thomas at gmx.de>
> Subject: [gmx-users] decorrelation function
> To: gmx-users at gromacs.org
> Message-ID: <20110126123857.156450 at gmx.net>
> Content-Type: text/plain; charset="utf-8"
>
> Hello!
>
> I have a question concerning decorrelation/autocorrelation functions:
>
> I studied the topic of autocorrelation function in Gromacs. For instance,
> I can define any distance between different atoms of my IL over time
> (g_dist) as *.xvg file. For g_analyze, I use this as input and plot the
> autocorrelation function (-av) and can fit it with -fitfn exp. But when I want to
> use the Legendre option -P 2 to get a second order legendre polynomial (which
> is used quite often in literature) the error appears:
>
> Incompatible mode bits: normal and vector (or Legendre)
>
> I think that I need vectors but this can not be done in Gromacs, does it?.
> How can I get Legendre functions, also for dihedrals?
>
> I'm looking forward to your answer! Thanks.
>
> Thomas
> --
> NEU: FreePhone - kostenlos mobil telefonieren und surfen!
> Jetzt informieren: http://www.gmx.net/de/go/freephone
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 26 Jan 2011 14:37:17 +0100
> From: Anna Marabotti <anna.marabotti at isa.cnr.it>
> Subject: [gmx-users] Re: Re: segmentation fault while running eneconv
> To: gmx-users at gromacs.org
> Message-ID: <01NX2ZQ6WGJ6OSSG15 at mx.isti.cnr.it>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Justin,
> thanks a lot for your suggestions. I checked the first 50ns simulation log
> files and in fact they start at zero and they don't say Gromacs is using
> checkpoints. Therefore, I'll follow your suggestions and discard the first
> 5ns simulations.
>
> Just to be sure about it: to use checkpoints for the continuation of a MD
> that has not crashed, are the followings the correct commands? (now I'm
> writing in general)
>
> tpbconv -s first_MD.tpr -extend desired_time_ps -o second_MD.tpr
>
> and
>
> mdrun -s second_MD.tpr -cpi first_MD.cpt -deffnm second_MD
>
> I was quite sure about it...until yesterday...
>
> Since I used the above format, if it is correct, the only other
> possibility
> is that I made a mistake in writing the correct name of the 5ns .cpi file.
> I
> see in the manual that if no checkpoint file is found, Gromacs restarts
> from
> the first step of the .tpr file. Could it be possible that I wrongly wrote
> the name of the .cpt file in the mdrun command and therefore Gromacs
> restarted from the first step? If this hypothesis is true, I leave just a
> little comment for developers: IMHO, it would be better if this option
> would
> be less "intelligent" (this is the definition of the manual) and stop the
> program claiming for the lack of the .cpt file, in case of such a
> mistake...
>
> Thanks to all and best regards
> Anna
> ____________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma, 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Email: anna.marabotti at isa.cnr.it
> Skype account: annam1972
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
>
> "When a man with a gun meets a man with a pen, the man with a gun is a
> dead
> man"
>
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> ------------------------------
>
> Message: 4
> Date: Wed, 26 Jan 2011 08:45:43 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Re: segmentation fault while running
> eneconv
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D402587.7050509 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Anna Marabotti wrote:
> > Dear Justin,
> > thanks a lot for your suggestions. I checked the first 50ns simulation
> > log files and in fact they start at zero and they don't say Gromacs
> > is using checkpoints. Therefore, I'll follow your suggestions and
> > discard the first 5ns simulations.
> >
> > Just to be sure about it: to use checkpoints for the continuation of a
> > MD that has not crashed, are the followings the correct commands? (now
> > I'm writing in general)
> >
> > tpbconv -s first_MD.tpr -extend desired_time_ps -o second_MD.tpr
> >
> > and
> >
> > mdrun -s second_MD.tpr -cpi first_MD.cpt -deffnm second_MD
> >
>
> A bit redundant ("mdrun -deffnm second_MD -ci first_MD.cpt" is all you
> need),
> but yes, correct.
>
> > I was quite sure about it...until yesterday...
> >
>
> That's why writing scripts to execute your commands is a good idea. You
> have an
> absolute record of what you typed.
>
> > Since I used the above format, if it is correct, the only other
> > possibility is that I made a mistake in writing the correct name of the
> > 5ns .cpi file. I see in the manual that if no checkpoint file is found,
> > Gromacs restarts from the first step of the .tpr file. Could it be
> > possible that I wrongly wrote the name of the .cpt file in the mdrun
> > command and therefore Gromacs restarted from the first step? If this
> > hypothesis is true, I leave just a little comment for developers: IMHO,
> > it would be better if this option would be less "intelligent" (this is
> > the definition of the manual) and stop the program claiming for the lack
> > of the .cpt file, in case of such a mistake...
> >
>
> True, if mdrun can't find your .cpt file, it starts the run from the
> beginning
> time in the .tpr file. I believe there may have been some relevant
> changes in
> the 4.5.x series (i.e. stopping when files are missing), but I think
> that's more
> related to the fact that, as of version 4.5, mdrun -append is the default
> behavior.
>
> -Justin
>
> > Thanks to all and best regards
> > Anna
> > ____________________________________________________
> > Anna Marabotti, Ph.D.
> > Laboratory of Bioinformatics and Computational Biology
> > Institute of Food Science, CNR
> > Via Roma, 64
> > 83100 Avellino (Italy)
> > Phone: +39 0825 299651
> > Fax: +39 0825 781585
> > Email: anna.marabotti at isa.cnr.it <mailto:anna.marabotti at isa.cnr.it>
> > Skype account: annam1972
> > Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
> >
> > "When a man with a gun meets a man with a pen, the man with a gun is a
> > dead man"
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> --
> 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/Support/Mailing_Lists/Search before posting!
>
> End of gmx-users Digest, Vol 81, Issue 204
> ******************************************
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