[gmx-users] Can not open file: topol.tpr
drugdesign
drugdesign at yandex.ru
Tue Mar 3 13:52:36 CET 2009
Oh, I am very sorry, I've copied the wrong error. Actually error was with the same tutorial at the next step with mdrun -v deffnm em.
I can't figure out why I need topol.tpr for energy minimization? It must be only em.tpr, right? by -v deffnm command?
-------------------------------------------------------
Program mdrun, VERSION 4.0.2
Source code file: gmxfio.c, line: 736
Can not open file:
topol.tpr
-------------------------------------------------------
"I Smell Smoke From a Gun Named Extinction" (Pixies)
andrew at linux-f29d:~/GROMACS_MD/1LYD> mdrun -v deffnm em
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Today's Topics:
1. Question (Elias santos)
2. tool.top does not found (drugdesign)
3. Re: tool.top does not found (Justin A. Lemkul)
4. help with FAD topology, please (Miguel Quiliano Meza)
5. Re: help with FAD topology, please (Justin A. Lemkul)
6. Re: Question (Mark Abraham)
7. RE: Cannot obtain the expected pressure using the
Parrinello-Rahman coupling in a gas-liquid system (Berk Hess)
----------------------------------------------------------------------
Message: 1
Date: Sun, 1 Mar 2009 09:14:36 -0300
From: Elias santos <silvasantosster at gmail.com>
Subject: [gmx-users] Question
To: gmx-users-request <gmx-users-request at gromacs.org>, gmx-users
<gmx-users at gromacs.org>
Message-ID:
<97baf6380903010414v50f35a14l47d66fbf020a2fdb at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi!!
I am changing my equipment for a AMD quad Core with two physical
processors and would like to know if in this configuration I will have
problems of compatibility with gromacs 4.0.
Elias Silva
------------------------------
Message: 2
Date: Sun, 01 Mar 2009 17:07:25 +0300
From: drugdesign <drugdesign at yandex.ru>
Subject: [gmx-users] tool.top does not found
To: gmx-users at gromacs.org
Message-ID: <29071235916445 at webmail45.yandex.ru>
Content-Type: text/plain; charset=KOI8-R
Dear GROMACS users,
I am trying to perform thе tutorial listed below with amber03 force field, but I get an error
about tool.top while running grompp with em.mdp
What can cause such a problem?
Best regards,
Andrew
https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
This is a command line:
andrew at linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c solvated.gro -o em.tpr
checking input for internal consistency...
-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 810
Fatal error:
tool.top does not exist
-------------------------------------------------------
"Baseball Heroes Only" (P.J. Harvey)
------------------------------
Message: 3
Date: Sun, 01 Mar 2009 09:54:11 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] tool.top does not found
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <49AAA193.4050303 at vt.edu>
Content-Type: text/plain; charset=KOI8-R; format=flowed
drugdesign wrote:
> Dear GROMACS users,
> I am trying to perform thе tutorial listed below with amber03 force field, but I get an error
> about tool.top while running grompp with em.mdp
> What can cause such a problem?
> Best regards,
> Andrew
>
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
>
> This is a command line:
>
> andrew at linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c solvated.gro -o em.tpr
>
> checking input for internal consistency...
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.2
> Source code file: grompp.c, line: 810
>
> Fatal error:
> tool.top does not exist
> -------------------------------------------------------
>
tool.top != topol.top; watch for typos!
-Justin
> "Baseball Heroes Only" (P.J. Harvey)
>
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Sun, 1 Mar 2009 11:42:04 -0500
From: Miguel Quiliano Meza <rifaximina at gmail.com>
Subject: [gmx-users] help with FAD topology, please
To: gmx-users at gromacs.org
Message-ID:
<6c2f55e30903010842g462991c8nf4fe6189dfb34e1c at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear all.
I am a new user of GROMACS, I have read the user book and free tutorials in
the WEB, but now when I try to do a simulation, appears FAD no topology, I
have been reading that PRODRG server is a way to achieve that goal, I tried
but the output format is different, it means old version (for gromos 96
forcefield).
I do not mind edit by hand (I want to learn), I searched in the gmx-users
but no one shares the FAD topology. Until now, I can't run my simulation.
So, I would be very grateful if someone could give me "tips", advices or the
FAD topology (in this way I could see my errors).
Thanks in advance.
Miguel.
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Message: 5
Date: Sun, 01 Mar 2009 11:53:14 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] help with FAD topology, please
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <49AABD7A.2030300 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Miguel Quiliano Meza wrote:
> Dear all.
>
> I am a new user of GROMACS, I have read the user book and free tutorials
> in the WEB, but now when I try to do a simulation, appears FAD no
> topology, I have been reading that PRODRG server is a way to achieve
> that goal, I tried but the output format is different, it means old
> version (for gromos 96 forcefield).
>
PRODRG will give ffgmx-compatible output, but PRODRG beta will give
Gromos96-compatible output. The latter is preferred, but in either case you
will have to manually alter the topology.
> I do not mind edit by hand (I want to learn), I searched in the
> gmx-users but no one shares the FAD topology. Until now, I can't run my
> simulation.
>
In the .rtp file of several Gromos96 force fields you will find a few different
FMN variants. This should provide you with a reasonable starting point for
creating your FAD topology (when you consider that ATP is also part of the force
field as well).
-Justin
> So, I would be very grateful if someone could give me "tips", advices or
> the FAD topology (in this way I could see my errors).
>
> Thanks in advance.
>
> Miguel.
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 6
Date: Mon, 02 Mar 2009 04:59:51 +1100
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Question
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <49AACD17.20503 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Elias santos wrote:
> Hi!!
>
> I am changing my equipment for a AMD quad Core with two physical
> processors and would like to know if in this configuration I will have
> problems of compatibility with gromacs 4.0.
No - MPI will be needed, but that is a non-issue.
Mark
------------------------------
Message: 7
Date: Sun, 1 Mar 2009 22:18:51 +0100
From: Berk Hess <gmx3 at hotmail.com>
Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
Parrinello-Rahman coupling in a gas-liquid system
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <BLU134-W328EB76CCB30D2D512D8F08EA80 at phx.gbl>
Content-Type: text/plain; charset="gb2312"
Hi,
But this has nothing to do with bug 165, does it?
If you have a surface, you have surface tension which tries to minimize the surface area.
That is what you should get and what you indeed do get; x/y get smaller, z gets larger,
decreasing the surface area.
If you have a x/y surface, you should keep the x/y sizes constant and only couple z.
Berk
From: guogj at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system
Date: Sun, 1 Mar 2009 05:09:39 +0000
Hi,
After I recheck the box, it is indeed the case described in bugzilla 165. The length of box increases in the Z-direction and decreases in the X/Y-direction with time. When I prolong the run, it exits abnormally at the time when the Box-X/Y reduces to a value less than 2*rvdw. When I fix the Box-Z by setting the compressibility as zero, the semiisotropic with P-R barostat produces the inaccurate pressure again. Now, I have to use the Berendsen barostat for my methane-water interface system.
Guang-Jun
> Date: Sat, 28 Feb 2009 19:53:10 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a gas-liquid system
>
> GuoGuangjun wrote:
> > Hi,
> >
> >
> > The question is resolved by changing the pcoupltype from isotropic to
> > semiisotropic. Correspondingly, the compressibility and ref_p are given
> > for the x/y and z directions with the same original values,
> > respectively. The test system includes 300 methane, 1725 water, and 300
> > methane, forming two interfaces parallel to the xy-plane. Now, the
> > accurate average-total-pressure is obtained from a short run (0.2 ns)
> > with the default tau_p (1 ps).
>
> Please be careful when you use this kind of pressure coupling, you may
> get the right pressure but you box might keep growing in one direction
> forever. See bugzilla 165. Actually I'm pretty sure it will.
> Unfortunately we don't really understand what is going on here.
> >
> >
> >
> > Thank you for your kind replies and useful clues.
> >
> > Guang-Jun
> >
> > ------------------------------------------------------------------------
> > From: gmx3 at hotmail.com
> > To: gmx-users at gromacs.org
> > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> > Parrinello-Rahman coupling in a gas-liquid system
> > Date: Sat, 28 Feb 2009 15:00:50 +0100
> >
> > Hi,
> >
> > Is 327 bar the averge total pressure or one the of components of the
> > pressure tensor?
> > You will have a surface tension acting in the system causing a
> > difference in the different components.
> >
> > Also it is still not completely clear to me how long you equilibrate and
> > average.
> > Also the results will depend very much on the size of the system.
> > In small systems the pressure fluctuations are enormous.
> > With Berendsen these fluctuations will be surpressed, with PR not.
> >
> > With PR I would use a tau_p of around 10 ps.
> > You might need to average the pressure over several (tens of?) ns (after
> > several ns of equilibration)
> > to obtain a good average.
> >
> > Berk
> >
> > ------------------------------------------------------------------------
> > From: guogj at hotmail.com
> > To: gmx-users at gromacs.org
> > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> > Parrinello-Rahman coupling in a gas-liquid system
> > Date: Sat, 28 Feb 2009 13:51:15 +0000
> >
> > Hi, Justin,
> >
> > Thanks for your rapid reply. Let me decribes the question in more details.
> > First ,two gaseous mathane systems and one liquid water system are
> > equilibrated at 300 bar and 250 K in advance. Then, the gas systems are
> > put at the both sides of liquid. The combined system is performed for
> > 3ns with the Parrinello-Rahman barostat, which produces a average
> > pressure of 327 bar. I am strange to the value and several tests are
> > run, mentioned previously. All these test runs take the end gro file of
> > the 3ns-run as the beginning. When the berendsen barostat is used,
> > the pressure is OK. When the Parrinello-Rahman barostat is used, the
> > questionary pressure occurs again. Although I will try to make a long
> > run for equilibrium, I think the equilibrium has reached because the
> > ~330 bar is always obtained no matter how long simulations are sampled,
> > from 0.2 ns to 3 ns. The version of Gromacs I used is 4.0.4. By the way,
> > how long did you equilibrate your membrane system and how many atoms
> > in it? Thanks again.
> >
> > Guang-Jun
> >
> >
> >
> > > Date: Sat, 28 Feb 2009 07:43:29 -0500
> > > From: jalemkul at vt.edu
> > > To: gmx-users at gromacs.org
> > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using
> > the Parrinello-Rahman coupling in a gas-liquid system
> > >
> > >
> > >
> > > GuoGuangjun wrote:
> > > > In fact, I once run the gas-liquid interface for 3 ns, the pressure is
> > > > still as high as 327 bar.
> > >
> > > There are two possibilities in my mind:
> > >
> > > 1. 3 ns is still not long enough.
> > > 2. Your gas phase is causing the problem. If the pressure is right
> > for water
> > > alone, then the problem likely comes from the inclusion of your gas
> > phase and
> > > whatever parameters you're using for whatever species you have in
> > this phase.
> > > Examine your parameters and consider how they were derived and
> > whether or not
> > > they are adequate.
> > >
> > > Also, what version of Gromacs are you using? There were some changes
> > made to
> > > the Parrinello-Rahman barostat between 3.3.x and 4.0.x.
> > >
> > > -Justin
> > >
> > > > Guang-Jun
> > > >
> > > >
> > > > > Date: Sat, 28 Feb 2009 07:19:30 -0500
> > > > > From: jalemkul at vt.edu
> > > > > To: gmx-users at gromacs.org
> > > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using
> > > > the Parrinello-Rahman coupling in a gas-liquid system
> > > > >
> > > > >
> > > > >
> > > > > GuoGuangjun wrote:
> > > > > >
> > > > > > Hi, All,
> > > > > > I am simulating an interface system composed of methane gas and
> > liquid
> > > > > > water in the NPT ensemble. The temperature is well controlled
> > by using
> > > > > > either the Berendsen or the Nose-Hoover T-couplings. As for
> > pressure,
> > > > > > the Berendsen P-coupling also works well. However, the
> > > > Parrinello-Rahman
> > > > > > P-coupling always produces a higher pressure than the expected. For
> > > > > > example, I set ref_p=300 bar in the mdp file but obtain an average
> > > > > > pressure as ~330 bar (over 0.5 ns). I test the tau_p in the range
> > > > 0.1 ~
> > > > > > 10 ps, the case does not change. When I test the sin! ! gle-phase
> > > > system,
> > > > > > i.e., pure water, the Parrinello-Rahman P-coupling can indeed
> > produce
> > > > > > the expected pressure with the deviation less than 2 bar. What
> > is the
> > > > > > matter in the two-phase system?
> > > > > >
> > > > >
> > > > > When I've used the Parrinello-Rahman barostat for membrane systems,
> > > > it works
> > > > > just fine. Perhaps 500 ps is too short of a timeframe to arrive at
> > > > the average.
> > > > > Heterogeneous systems often take longer to equilibrate.
> > > > >
> > > > > -Justin
> > > > >
> > > > > > Thanks a lot.
> > > > > > Guang-Jun
> > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > > СЂПЬЯТди MSN БЃЛЄЖмЃЌБЃеЯ MSN АВШЋЮШЖЈЃЁ ЯждкОЭЯТдиЃЁ
> > > > > > <http://im.live.cn/safe/>
> > > > > >
> > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------
> > > > > >
> > > > > > _______________________________________________
> > > > > >! ! ; gmx-users mailing list gmx-users at gromacs.org
> > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
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> > > > >
> > > > > --
> > > > > ========================================
> > > > >
> > > > > Justin A. Lemkul
> > > > > Graduate Research Assistant
> > > > > 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://www.gromacs.org/mailman/listinfo/gmx-users
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> > > > posting!
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> > > >
> > > >
> > ------------------------------------------------------------------------
> > > > ФуКЭФуЕФАЎШЫЖМШЅЙ§ФФРяЃППьРДЮЂШэЕиЭМвЛЦ№ЛцжЦАЎЕФЕиЭМАЩЃЁ СЂМДВщПДЃЁ
> > > > <http://ditu.live.com/?form=MICHAJ >
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Graduate Research Assistant
> > > 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
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> > <http://ditu.live.com/?form=MICHAJ>
> > ------------------------------------------------------------------------
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> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> _______________________________________________
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