[gmx-users] Re: gmx-users Digest, Vol 42, Issue 47
Li Zhenhai
shibalagu.thu at gmail.com
Fri Oct 12 16:51:59 CEST 2007
Hello, Jian Yin
Thanks for your help. I have solved my problem just now.
Li Zhenhai
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
China
Tel: 86-10-62773779
E-mail: shibalagu.thu at gmail.com
2007-10-12
======= 2007-10-12 22:04:31 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======
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>Today's Topics:
>
> 1. Re: *** GMX Spamverdacht *** [gmx-users] Constraining to
> fixed position (Martin H?fling)
> 2. Re: Compiling GROMACS with FORTRAN? (Ivano Eberini)
> 3. Calculating the energy of one molecule in the (Li Zhenhai)
> 4. (no subject) (sarbani chattopadhyay)
> 5. Re: (no subject) (Carsten Kutzner)
> 6. Re: non-existent angles found from trajectory g_angle
> (Mark Abraham)
> 7. RE: Calculating the energy of one molecule in
> themulti-molecule system (Yin Jian)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 12 Oct 2007 12:15:56 +0200
>From: "Martin H?fling" <martin.hoefling at gmx.de>
>Subject: Re: *** GMX Spamverdacht *** [gmx-users] Constraining to
> fixed position
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <20071012101556.105220 at gmx.net>
>Content-Type: text/plain; charset="us-ascii"
>
>...ok i misunderstood the com_t0 option. I'll try to introduce a virtual particle without interactions, define a group on this and constrain the protein distance to the particle.
>
>Best
>Martin
>--
>Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten
>Browser-Versionen downloaden: http://www.gmx.net/de/go/browser
>
>
>------------------------------
>
>Message: 2
>Date: Fri, 12 Oct 2007 12:31:15 +0200
>From: Ivano Eberini <ivano.eberini at unimi.it>
>Subject: Re: [gmx-users] Compiling GROMACS with FORTRAN?
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <ED0B290C-CE0D-4E4A-8038-3B63F36488B4 at unimi.it>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Il giorno 12/ott/07, alle ore 11:29, David van der Spoel ha scritto:
>
>> Ivano Eberini wrote:
>>> Dear all,
>>> we have just installed GROMACS-3.3.2 on a BlueGene (BG/L) cluster,
>>> compiling it without FORTRAN.
>>> Do you deem it could be better to recompile it adding "--enable-
>>> fortran"?
>> the proof of the pudding is in the eating.
>> please try it.
>>
>
>Dear David,
>here are the results for two runs (full.mdp in speptide folder of
>GROMACS tutorial) with 16 chips / 32 tasks on BG/L,
>
>without FORTRAN:
>
>
> NODE (s) Real (s) (%)
> Time: 161.000 161.000 100.0
> 2:41
> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>Performance: 12.529 3.034 5.366 4.472
>
>
>with FORTRAN:
>
> NODE (s) Real (s) (%)
> Time: 155.000 155.000 100.0
> 2:35
> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>Performance: 13.021 3.143 5.574 4.306
>
>Best regards,
>Ivano
>--
>Ivano Eberini
>Gruppo di Studio per la Proteomica e la Struttura delle Proteine
>Dipartimento di Scienze Farmacologiche
>Universit?degli Studi di Milano
>Via Giuseppe Balzaretti, 9
>20133 - Milano
>tel.: +39-02-50318395, fax: +39-02-50318284
>
>"Quelli che scavano il sole, cercando un'ombra migliore"
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>------------------------------
>
>Message: 3
>Date: Fri, 12 Oct 2007 18:33:47 +0800
>From: "Li Zhenhai" <shibalagu.thu at gmail.com>
>Subject: [gmx-users] Calculating the energy of one molecule in the
>To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>Message-ID: <470f4db2.17bb720a.2ca1.ffffc4ff at mx.google.com>
>Content-Type: text/plain; charset="gb2312"
>
>Hello, Xavier Periole
>
> I have resolved my problem. Thanks for your help. You are so kind!
>
>Li Zhenhai
>Department of Engineering Mechanics
>Tsinghua University
>Beijing 100084
>China
>Tel: 86-10-62773779
>E-mail: shibalagu.thu at gmail.com
>
>2007-10-12
>
>======= 2007-10-11 21:26:32 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======
>
>
>>------------------------------
>>
>>Message: 2
>>Date: Thu, 11 Oct 2007 14:25:35 +0200
>>From: "Xavier Periole" <X.Periole at rug.nl>
>>Subject: Re: [gmx-users] Calculating the energy of one molecule in the
>> multi-molecule system
>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>Message-ID: <web-56146831 at mail3.rug.nl>
>>Content-Type: text/plain;charset=utf-8;format="flowed"
>>
>>
>>To get the bonded energy terms of one molecule in your system you
>>have to generate a trajectory file containing this molecule only:
>>
>>trjconv -f full.trr -n molecule.ndx -o molecule.trr
>>
>>and then rerun the simulation using a tpr containing only the topology
>>of your molecule:
>>
>>grompp -f molecule.mdp -c molecule.gro -o molecule.tpr
>>mdrun -rerun molecule.trr -s molecule.tpr
>>
>>Notes:
>>1- you MUST use the a trr trajectory (full precision). the coordinates
>>in xtc files are not precise enough.
>>2- the molecule.mdp should be identical to the original one except
>>for the update of the neighbor list (nstlist = 1) and print energies
>>every step (nstenergy).
>>
>>
>>On Thu, 11 Oct 2007 16:59:43 +0800
>> "shibalagu" <shibalagu.thu at gmail.com> wrote:
>>> Hi, all,
>>>
>>> I did a simulation on a system which had more than one molecule in it. After
>>>the simulation, I want to check the bond/angle/dihedral energy of one
>>>molecule in the system.
>>>
>>> So I set a energy_grp named DNA in the mdp file, and used the command
>>>g_energy to calculate the energy on the energy_grp DNA. But I found that if I
>>>set a energy_grp in the mdp file, I still can only calculate the LJ/Coul
>>>energy on the molecule, and the bond/angle energy on the whole system,
>>>without the bond or angle energy on the molecule separately.
>>>
>>> Does anyone can help me? Thanks a lot!
>>>
>>>
>>> Li Zhenhai
>>> Department of Engineering Mechanics
>>> Tsinghua University
>>> Beijing 100084
>>> China
>>> Tel: 86-10-62773779
>>> E-mail: shibalagu.thu at gmail.com
>>>
>>> 2007-10-11
>>>
>>> _______________________________________________
>>> 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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>>
>>-----------------------------------------------------
>>XAvier Periole - PhD
>>
>>1- Institute of Molecular Assemblies
>> City University of New York - USA
>>2- Molecular Dynamics-Group
>> University of Groningen - The Netherlands
>>http://md.chem.rug.nl/~periole
>>-----------------------------------------------------
>>
>>
>
>
>------------------------------
>
>Message: 4
>Date: 12 Oct 2007 11:14:29 -0000
>From: "sarbani chattopadhyay" <sarbani_c84 at rediffmail.com>
>Subject: [gmx-users] (no subject)
>To: gmx-users at gromacs.org
>Message-ID: <20071012111429.31766.qmail at f5mail35.rediffmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
> hi,
> I am using gromacs to run MD simulations using "Intel dual core machine OSX (version
>10.4.10) ".I downloaded the 'already compiled gromacs package'. Is there any way to find
>whether the simulation process makes optimum usage of the 2 processors.
>Is there any command to direct the 'mdrun' that takes the optimum advantage of the
>available processors?
>
>We have another machine which has "Xeon Quad Core ,the MAC version being 10.4.10.
>How to run gromacs making optimum usage of the 4 processors?
>
>Is there any method to use "XGRID" built in OSX?
>
>Any suggestions are welcome.Thanks
>
>Sarbani
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>------------------------------
>
>Message: 5
>Date: Fri, 12 Oct 2007 13:37:22 +0200
>From: Carsten Kutzner <ckutzne at gwdg.de>
>Subject: Re: [gmx-users] (no subject)
>To: sarbani chattopadhyay <sarbani_c84 at rediffmail.com>, Discussion
> list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <470F5C72.7040402 at gwdg.de>
>Content-Type: text/plain; charset=ISO-8859-1
>
>sarbani chattopadhyay wrote:
>> hi,
>> I am using gromacs to run MD simulations using "Intel dual core
>> machine OSX (version
>> 10.4.10) ".I downloaded the 'already compiled gromacs package'. Is there
>> any way to find
>> whether the simulation process makes optimum usage of the 2 processors.
>
>Hi Sarbani,
>
>I assume you have the MPI version of Gromacs. You could for example run
>a 1000-step simulation on 1 CPU and afterwards on 2 CPUs. Gromacs prints
>performance numbers at the end of the md0.log file. You could then
>divide the ns/day value of your 2 CPU run by two times that value of the
>1 CPU run and receive a measure for the scaling, which should not be
>much lower than 1.00 on a dual or quad core machine. Use longer runs for
>more reliable numbers. But a 10 minute run or so should suffice.
>
>> Is there any command to direct the 'mdrun' that takes the optimum
>> advantage of the
>> available processors?
>
>You might want to use the -shuffle and -sort options together with
>setting the number of CPUs by -np in the preprocessor grompp.
>
>> We have another machine which has "Xeon Quad Core ,the MAC version being
>> 10.4.10.
>> How to run gromacs making optimum usage of the 4 processors?
>
>mpirun -np 4 mdrun -s x.tpr
>
>Hope that helps,
>Regards,
> Carsten
>
>
>
>--
>Dr. Carsten Kutzner
>Max Planck Institute for Biophysical Chemistry
>Theoretical and Computational Biophysics Department
>Am Fassberg 11
>37077 Goettingen, Germany
>Tel. +49-551-2012313, Fax: +49-551-2012302
>http://www.mpibpc.mpg.de/research/dep/grubmueller/
>http://www.gwdg.de/~ckutzne
>
>
>------------------------------
>
>Message: 6
>Date: Fri, 12 Oct 2007 23:52:07 +1000
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] non-existent angles found from trajectory
> g_angle
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <470F7C07.5090303 at anu.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Sampo Karkola wrote:
>> Hi Mark,
>>
>> visualisation of the .trr file with vmd succeeded, but the original
>> problem remains.The -pbc cluster option did not do any better. The weird
>> thing is that after trjconv with -pbc cluster, -center tric and -ur
>> compact (or without the latter two) produces a trajectory with the
>> ligand in the correct position but some of the surface atoms of the
>> protein jump between the boxes. If I then do trjconv with -fit
>> progressive (or rot+trans) the protein is displayed as a whole but the
>> ligand jumps out of the box. I've used the protein_heme_ligand group in
>> the index file as the centering, clustering and fitting group.
>>
>> And in all cases I see the weird angles at 50 deg, which are not shown
>> in vmd visualising the system with ligand staying in the cavity.
>
>Well, find out what frames have these occurring and see why it is.
>
>Mark
>
>
>------------------------------
>
>Message: 7
>Date: Fri, 12 Oct 2007 22:03:46 +0800
>From: "Yin Jian" <smayinj at nus.edu.sg>
>Subject: RE: [gmx-users] Calculating the energy of one molecule in
> themulti-molecule system
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Message-ID:
> <54D4A84918540944843542B9BB802E4E0155EA75 at MBX03.stf.nus.edu.sg>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi Zhenhai,
>anyway the bonded(bond lengths, bond angles, and dihedral angles) and
>nonbond energies can be calculated by hand with the geometry information
>
>stored in pdb (xtc/trr) and the force field parameters.
>
>Regards,
>Jian Yin
>
>Research Staff
>E5-04-19
>Singapore-MIT Alliance (SMA)
>National University of Singapore
>Singapor
>
>
>-----Original Message-----
>From: gmx-users-bounces at gromacs.org
>[mailto:gmx-users-bounces at gromacs.org] On Behalf Of shibalagu
>Sent: Thursday, October 11, 2007 5:00 PM
>To: gmx-users
>Subject: [gmx-users] Calculating the energy of one molecule in
>themulti-molecule system
>
>Hi, all,
>
>I did a simulation on a system which had more than one molecule in it.
>After the simulation, I want to check the bond/angle/dihedral energy of
>one molecule in the system.
>
>So I set a energy_grp named DNA in the mdp file, and used the command
>g_energy to calculate the energy on the energy_grp DNA. But I found that
>if I set a energy_grp in the mdp file, I still can only calculate the
>LJ/Coul energy on the molecule, and the bond/angle energy on the whole
>system, without the bond or angle energy on the molecule separately.
>
>Does anyone can help me? Thanks a lot!
>
>
>Li Zhenhai
>Department of Engineering Mechanics
>Tsinghua University
>Beijing 100084
>China
>Tel: 86-10-62773779
>E-mail: shibalagu.thu at gmail.com
>
>2007-10-11
>
>_______________________________________________
>gmx-users mailing list gmx-users at gromacs.org
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>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>------------------------------
>
>_______________________________________________
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>End of gmx-users Digest, Vol 42, Issue 47
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