[gmx-users] Virial Calculation
David van der Spoel
spoel at xray.bmc.uu.se
Tue Feb 7 16:38:29 CET 2006
Tandia, Adama wrote:
> Dear ALL:
>
> I would like to nail down the questions I have regarding the calculation of the virial in Gromacs 3.2.1.
>
> When one uses g_energy to calculate virial_XX, virial_YY and virial_ZZ and then use:
First off, g_energy does not calculate the virial, it merel prints what
is in the edr file. You can check the contents more directly with gmxdump.
> virial = (1/3)*(virial_XX + virial_YY + virial_ZZ),
> is this value equal to -0.5 * Sum_{i<j} [r x F] or not?
It should be, but the forces necessary for computing the virial
components are only available internally in mdrun (in particular the
components due to constraints and PME).
>
> Thanks
>
> Adama
>
> Adama Tandia
> Modeling & Simulation
> Corning INC
> SP TD 01-01
> Corning NY 14831 USA
> Tel: 607 248 1036
> Fax: 607 974 3405
> www.corning.com
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of gmx-users-request at gromacs.org
> Sent: Tuesday, February 07, 2006 9:14 AM
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 22, Issue 30
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> Today's Topics:
>
> 1. Re: dummy atoms for amber free energy (Berk Hess)
> 2. RE: stochastic thermostat (Berk Hess)
> 3. pressure coupling (ninoo mani)
> 4. Re: still g_order problem! (Alan Dodd)
> 5. Re: pressure coupling (Mark Abraham)
> 6. Inconsistent shift warning in g_traj (Janne Hirvi)
> 7. Re: Inconsistent shift warning in g_traj (David van der Spoel)
> 8. Re: Inconsistent shift warning in g_traj (Xavier Periole)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 07 Feb 2006 14:06:28 +0100
> From: "Berk Hess" <gmx3 at hotmail.com>
> Subject: Re: [gmx-users] dummy atoms for amber free energy
> To: gmx-users at gromacs.org
> Message-ID: <BAY110-F31E66396508DFA9B3973888E010 at phx.gbl>
> Content-Type: text/plain; format=flowed
>
>
>
>
>
>>From: Maik Goette <mgoette at mpi-bpc.mpg.de>
>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>Subject: Re: [gmx-users] dummy atoms for amber free energy
>>Date: Tue, 07 Feb 2006 10:56:46 +0100
>>
>>Hi David
>>
>>That's also a point of discussion in our group.
>>My personal opinion is, that a mass, which is connected via e.g. the
>>bond
>>potential would fluctuate in the harmonic function and those energy terms
>>should cancel out over time. For the dummy-masses have no other
>>interactions, there won't occur any frictional energy contribution.
>>So everything should be fine.
>>Anyway, grompp don't like 0 masses. This may be, because F/m=a and this
>>would lead to a division with 0, which isn't defined. I never tried to
>>compare a run with full dummy masses and masses set to small values, e.g.
>>0.001.
>>
>>For this is very intuitive, I would be very thankful for every hint to
>>literature regarding this aspect.:)
>
>
> I don't think this is what David meant.
> Masses only affect kinetic properties.
> They do not enter in thermodynamics and therefore
> have no influence on the free-energy.
>
> The issue here is if the bonded interaction with the otherwise dummy masses affect the free energy. Well, if these bonded interaction do not couple to the rest of the system not. In most cases you will have one or more dummy atoms connected only by one bond to the rest of the molecule. Then the bond, angle and dihedral interactions do not affect the ensemble of the rest of the system. Problems occur when you would for instance eliminate one atom in a phenyl ring. Then it is clear that the bonded interactions with the dummy do affect the ensemble of the rest of the system.
>
> Berk.
>
>
>
>>Regards
>>
>>Maik Goette, Dipl. Biol.
>>Max Planck Institute for Biophysical Chemistry
>>Theoretical & computational biophysics department
>>Am Fassberg 11
>>37077 Goettingen
>>Germany
>>Tel. : ++49 551 201 2310
>>Fax : ++49 551 201 2302
>>Email : mgoette[at]mpi-bpc.mpg.de
>> mgoette2[at]gwdg.de
>>WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
>>
>>
>>David Mobley wrote:
>>
>>>Just out of curiousity, since you seem to know something about this,
>>>Maik... If you don't turn off the mass, doesn't it mean that there are
>>>energetic contributions from (for example) bond vibrations and things
>>>which are still left in in the end state? I usually do absolute binding
>>>free energy calculations so I'm not too up on how people correct for the
>>>fact that they have non-interacting dummy atoms which are still bonded to
>>>things in the end state.
>>>
>>>Thanks,
>>>David
>>>
>>>
>>>On 2/6/06, *Maik Goette* <mgoette at mpi-bpc.mpg.de
>>><mailto:mgoette at mpi-bpc.mpg.de>> wrote:
>>>
>>> Hi Matt
>>>
>>> I am not sure, if there may occur errors because of MW is used as
>>> water-dummy.
>>> But it's really no big deal to insert a DUM with 0 mass and charge.
>>> You can also create as much dummies with the masses you want as you
>>> like.
>>> If you like, I can send you my entries...but as I said, it's
>>>really
>>>no
>>> problem to make some.
>>> Nevertheless, you shouldn't make the mass disappear. just turn of VdW
>>> and electorstatics.
>>>
>>> Regards
>>>
>>> Maik Goette, Dipl. Biol.
>>> Max Planck Institute for Biophysical Chemistry
>>> Theoretical & computational biophysics department
>>> Am Fassberg 11
>>> 37077 Goettingen
>>> Germany
>>> Tel. : ++49 551 201 2310
>>> Fax : ++49 551 201 2302
>>> Email : mgoette[at]mpi- bpc.mpg.de <http://bpc.mpg.de>
>>> mgoette2[at]gwdg.de
>>> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
>>>
>>>
>>> mernst at tricity.wsu.edu <mailto:mernst at tricity.wsu.edu> wrote:
>>> > Dear gmx-users,
>>> >
>>> > The Pande group amber port does not contain any specially
>>> designated dummy atom type
>>> > like DUM. It does however contain atom types that seem very
>>> similar, like MW. I have
>>> > used MW as a dummy in a simulation where a hydrogen disappears
>>> (turns into a dummy
>>> > atom), assigning it zero charge as well. Is this a reasonable
>>> substitution? It is my
>>> > understanding that dummy atoms should have zero mass, zero
>>> charge, and zero vdw
>>> > interactions, and that their bonded interactions are unimportant
>>> (can duplicate
>>> > parameters of the atoms they are replacing) since in any case
>>> they will have no
>>> > energetic impact, being massless in their final state. Of course
>>> there are no long-range
>>> > interactions either with dispersion and electrostatic effects set
>>> to zero.
>>> >
>>> > Finally, I would like to thank everyone who has responded to my
>>> questions over the last
>>> > few days. Your help has been invaluable in getting me up to speed
>>> in this new simulation
>>> > environment.
>>> >
>>> > Matt Ernst
>>> > Washington State University
>>> >
>>> > _______________________________________________
>>> > gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
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>>>
>>>----------------------------------------------------------------------
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>>_______________________________________________
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>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 07 Feb 2006 14:07:53 +0100
> From: "Berk Hess" <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] stochastic thermostat
> To: gmx-users at gromacs.org
> Message-ID: <BAY110-F1868C8A30DB78D176A731C8E010 at phx.gbl>
> Content-Type: text/plain; format=flowed
>
>
>
>
>
>>From: "Dmitry Nerukh" <dn232 at cam.ac.uk>
>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>To: <gmx-users at gromacs.org>
>>Subject: [gmx-users] stochastic thermostat
>>Date: Tue, 7 Feb 2006 11:56:17 -0000
>>
>>Dear gromacs developers,
>>
>>
>>
>>Can you, please, describe the steps for running a normal molecular
>>dynamics with a stochastic thermostat? I have a very simple system -
>>just 2 waters in vacuum. I've tried setting the integrator to 'sd' and 'tau_t' to 0.
>>The
>>integration failed. Is it possible to have a stochastic dynamics with the
>>velocity friction term set to 0?
>
>
> No.
> The random and friction forces are linked by the fluctuation-dissipation
> theorem.
>
> Berk.
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 7 Feb 2006 13:02:26 +0000 (GMT)
> From: ninoo mani <ninoomani at yahoo.co.in>
> Subject: [gmx-users] pressure coupling
> To: gmx-users at gromacs.org
> Message-ID: <20060207130226.20297.qmail at web8414.mail.in.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Dear gmx users
> I have recently started using GROMACS. I have a little
> doubt about few concepts.
> In mdrun consider two systems 1. Peridic boundary
> condition on, temperature coupling on and no pressure
> coupling.
> 2. Periodic boundary condition on, temperature
> coupling on and pressure coupling on.
> What are the differences between these two systems?
> Thanks
> Ninoo
>
>
>
> __________________________________________________________
> Yahoo! India Matrimony: Find your partner now. Go to http://yahoo.shaadi.com
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 7 Feb 2006 05:16:26 -0800 (PST)
> From: Alan Dodd <anoddlad at yahoo.com>
> Subject: Re: [gmx-users] still g_order problem!
> To: gmx-users at gromacs.org
> Message-ID: <20060207131626.66828.qmail at web36503.mail.mud.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> You need a seperate group for each carbon atom along
> the chain... You can average multiple chains by
> letting each group have equivalent atoms from multiple
> chains, but unless you have at least 3 groups in your
> index file, you'll never get an order parameter out.
> Search through the mailing list archive, this has been described in some detail a couple of times.
>
> --- Rongliang Wu <wurl04 at iccas.ac.cn> wrote:
>
>
>>Hello gmx-users,
>>
>> i have made a index file of carbon atoms as
>>follows:
>>[ CAE ]
>> 5 15 25 35 45 55 65 75 85 95
>>105 115 125 135 145
>> 155 165 175 185 195 205 215 225 235 245
>>255 265 275 285 295
>> 305 315 325 335 345 355 365 375 385 395
>>405 415 425 435 445
>> 455 465 475 485 495 505 515 525 535 545
>>555 565 575 585 595
>> 605 615 625 635 645 655 665 675 685 695
>>705 715 725 735 745
>> 755 765 775 785 795 805 815 825 835 845
>>855 865 875 885 895
>> 905 915 925 935 945 955 965 975 985 995
>>
>>and used the command "g_order -f traj.trr -s
>>dwmd.tpr -szonly -n -sl 8" to calculate the order
>>parameters of atoms in the index file, but the
>>results are all 0 for each slices. but the system
>>was apparently not amorphous. are there any possible
>>mistakes for my procedure.
>>
>>
>>yes,the order parameters calculated in the previous
>>method are average over time and molecules.the order parameters can
>>also be calculated (and are all 0 for each slices) if i put all carbon
>>atoms in the index file. what this order parameter will be? average
>>over atoms?
>>
>>Thanks!
>>
>>Regards!
>>
>>Sincerely,
>>
>>Rongliang Wu
>>State Key Laboratory
>>of Polymer Physics and Chemistry
>>Center of Molecular Science
>>Institute of Chemistry
>>Chinese Academy of Sciences
>>
>>
>>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡wurl04 at iccas.ac.cn
>>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2006-02-07
>>
>>>_______________________________________________
>>
>>gmx-users mailing list gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
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>>list. Use the
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> ------------------------------
>
> Message: 5
> Date: Wed, 08 Feb 2006 00:31:33 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] pressure coupling
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <43E8A135.7040500 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> ninoo mani wrote:
>
>>Dear gmx users
>>I have recently started using GROMACS. I have a little
>>doubt about few concepts.
>>In mdrun consider two systems 1. Peridic boundary
>>condition on, temperature coupling on and no pressure
>>coupling.
>>2. Periodic boundary condition on, temperature
>>coupling on and pressure coupling on.
>>What are the differences between these two systems?
>
>
> I think reading the gromacs manual on pressure coupling would be helpful
> here.
>
> Mark
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 7 Feb 2006 16:03:39 +0200
> From: Janne Hirvi <janne.hirvi at joensuu.fi>
> Subject: [gmx-users] Inconsistent shift warning in g_traj
> To: gmx-users at gromacs.org
> Message-ID: <1139321019.43e8a8bb7636f at wwwmail.joensuu.fi>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello!
>
> I have tried to figure out method for calculation of the friction coefficient
> between graphite surfaces. I have simulated two infinite graphite surfaces with
> option pbc=full and everything seemed to be working properly. However, when I
> tried to extract coordinates, velocities, and forces of the center of mass of
> the graphite plane with g_traj (using option -com) I got numerous warnings
> about the inconsistent shifts:
>
> THERE WERE 198 INCONSISTENT SHIFTS. CHECK YOUR TOPOLOGY.
>
> I think that my topology-file for infinite graphite surface is correct and I
> would like to know what does this "warning" really mean and can I trust the
> results from g_traj anyway?
>
>
> Thanks for any help or comments!
>
> Janne
>
> ------------------------------------------------------------------------------
> Janne Hirvi, MSc(Physical Chemistry), Researcher
> University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
> Tel: +358 13 2514544 & +358 50 3474223
> E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
> ------------------------------------------------------------------------------
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 07 Feb 2006 15:09:34 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Inconsistent shift warning in g_traj
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <43E8AA1E.5050300 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Janne Hirvi wrote:
>
>>Hello!
>>
>>I have tried to figure out method for calculation of the friction coefficient
>>between graphite surfaces. I have simulated two infinite graphite surfaces with
>>option pbc=full and everything seemed to be working properly. However, when I
>>tried to extract coordinates, velocities, and forces of the center of mass of
>>the graphite plane with g_traj (using option -com) I got numerous warnings
>>about the inconsistent shifts:
>>
>>THERE WERE 198 INCONSISTENT SHIFTS. CHECK YOUR TOPOLOGY.
>>
>>I think that my topology-file for infinite graphite surface is correct and I
>>would like to know what does this "warning" really mean and can I trust the
>>results from g_traj anyway?
>
> This is because g_traj does PBC anyway in the old way. For velocities
> and forces this shouldn't matter. For coordinates it could, but this is
> periodic anyway, so it may not be very informative.
>
>
>>
>>Thanks for any help or comments!
>>
>>Janne
>>
>>------------------------------------------------------------------------------
>>Janne Hirvi, MSc(Physical Chemistry), Researcher
>>University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
>>Tel: +358 13 2514544 & +358 50 3474223
>>E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
>>------------------------------------------------------------------------------
>>_______________________________________________
>>gmx-users mailing list gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>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
>
>
>
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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