[gmx-users] RE: gmx-users digest, Vol 1 #1361 - 13 msgs

Warren DeLano warren at delanoscientific.com
Thu Apr 1 23:22:01 CEST 2004


Ack, sorry about that guys -- replied to the wrong email -- serves me right
for using Microsoft products.

> -----Original Message-----
> From: gmx-users-admin at gromacs.org 
> [mailto:gmx-users-admin at gromacs.org] On Behalf Of 
> gmx-users-request at gromacs.org
> Sent: Thursday, April 01, 2004 1:09 PM
> To: gmx-users at gromacs.org
> Subject: gmx-users digest, Vol 1 #1361 - 13 msgs
> 
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> specific than "Re: Contents of gmx-users digest..."
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> 
> Today's Topics:
> 
>    1. About  Temperature Calculation (Ane Xu)
>    2. Re: About  Temperature Calculation (Xavier Periole)
>    3. Trajectory to .pdb (ankur gupta)
>    4. Re: Trajectory to .pdb (Peter Zoon)
>    5. FW: [gmx-users] About  Temperature Calculation (Ane Xu)
>    6. Re: FW: [gmx-users] About  Temperature Calculation 
> (Xavier Periole)
>    7. RE:  About  Temperature Calculation (Ane Xu)
>    8. Re: About  Temperature Calculation (Xavier Periole)
>    9. RE:  About  Temperature Calculation (David)
>   10. Re: left-hand warnings? (xiaobing tian)
>   11. Re: left-hand warnings? (David)
>   12. Re: Trajectory to .pdb (Itamar Kass)
>   13. Re: Force Fields and Electrostatics (Dallas Warren)
> 
> --__--__--
> 
> Message: 1
> From: "Ane Xu" <xzp02 at mails.tsinghua.edu.cn>
> To: <gmx-users at gromacs.org>
> Date: Fri, 2 Apr 2004 20:56:35 +0800
> Subject: [gmx-users] About  Temperature Calculation
> Reply-To: gmx-users at gromacs.org
> 
> Dear All:
>     I am conducting simulation on carbon nanotubes, two 
> nanotubes is considered as a molecule and periodic boundary 
> condition is applied, I initiated the system with 300K by set 
> gen-temp=300, while after simulation, I found that the 
> temperature at step0 is 500K, but temperature of following 
> steps calculated by g_energy is only about 160K, so I have 
> two questions, I wish someone can help me to solve it.
> 
> 1) Why the temperature of following steps is so much lower 
> that of the initial step.
> 
> 2) How do g_energy calculate temperatures in such a system as 
> mine, i.e., structure A and B is connected by VDW 
> interaction, they belong to ONE molecule, but their COM may 
> have oppsite motion. Does the velocity of all atoms need to 
> minus the COM velocity of the whole system or the COM of 
> their sub-structure seperatly (A or B).
> 
>      BTW, this mailist is so helpful to me, thanks a lot,.
> 
> Ane
> 
> ---------------------------------------------
> Ane Xu ( Xu ZhiPing )
> Ph.D Candidate
> Office: 3-405
> Tel    : +86-10-627-83814
> Department of Enginnering Mechanics
> Tsinghua University
> Beijing, CHINA, 100084
> --------------------------------------------- 
> 
> 
> --__--__--
> 
> Message: 2
> Date: Thu, 01 Apr 2004 14:59:39 +0200
> From: Xavier Periole <x.periole at chem.rug.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] About  Temperature Calculation
> Reply-To: gmx-users at gromacs.org
> 
> 
> Do you have a solvent ? Which algorithm do you use to control 
> the temperature ?
> 
> XAvier
> 
> 
> 
> --__--__--
> 
> Message: 3
> Date: Thu, 1 Apr 2004 18:41:33 +0530 (IST)
> From: ankur gupta <ankurgup at iitk.ac.in>
> To: gmx-users at gromacs.org
> cc: gmx-users at gromacs.org
> Subject: [gmx-users] Trajectory to .pdb
> Reply-To: gmx-users at gromacs.org
> 
> Dear Gromacs Users,
> I have the run the simulation of protein in water and now I 
> want to convert the final trajectory file(.trr) to .pdb file. 
> Please guide me how can I do that?
> 
> Sincerely
> Ankur
> 
> 
> 
> 
> "You are making progress if each mistake You make is a new one"
>                                  \ 0 0 /
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>                         A A  N N N K K  U   U R R R
>                        A A N N N N K  K UUUUU R   R
> 
>                                ANKUR GUPTA
>                      FIFTH YEAR UNDERGRADUATE STUDENT
>                            ROOM NO B-208,HALL 1
>                       INDIAN INSTITUTE OF TECHNOLOGY
>                                KANPUR,INDIA
>                         PHONE:++91-512-597311,111
>                            FAX:++91-512-590007
>  
> **************************************************************
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>                                /           \
> 
> 
> 
> 
> 
> 
> 
> 
> 
> --__--__--
> 
> Message: 4
> Date: Thu, 1 Apr 2004 15:44:57 +0200
> To: gmx-users at gromacs.org
> From: Peter Zoon <zoon at science.uva.nl>
> Subject: Re: [gmx-users] Trajectory to .pdb
> Reply-To: gmx-users at gromacs.org
> 
> You could do that with trjconv, and then export evry frame to pdb.
> Keep in mind that the fileszie will increase dramatically !
> If its only 1 structure it doesn't matter, but if you want to 
> convert the whole trajectory I couldn't see why you would 
> want to do that.
> 
> Cheers
> Peter
> 
> >Dear Gromacs Users,
> >I have the run the simulation of protein in water and now I want to 
> >convert the final trajectory file(.trr) to .pdb file. Please 
> guide me 
> >how can I do that?
> >
> >Sincerely
> >Ankur
> >
> 
> 
> --__--__--
> 
> Message: 5
> From: "Ane Xu" <xzp02 at mails.tsinghua.edu.cn>
> To: <gmx-users at gromacs.org>
> Subject: FW: [gmx-users] About  Temperature Calculation
> Date: Fri, 2 Apr 2004 21:48:42 +0800
> Reply-To: gmx-users at gromacs.org
> 
> This is a multi-part message in MIME format.
> 
> ------=_NextPart_000_000C_01C418FC.4459D660
> Content-Type: text/plain;
> 	charset="US-ASCII"
> Content-Transfer-Encoding: 7bit
> 
> Dear XAvier:
> 
>     No solvent, no temperature coupling, just a NVE 
> simulation with gen_temp=300. 
>     Thanks.
>     BTW: why can not I reply the mail with attachment?
> 
> ZP
> 
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> On Behalf Of Xavier Periole
> Sent: 2004?4?1? 21:00
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] About Temperature Calculation
> 
> 
> 
> Do you have a solvent ? Which algorithm do you use to control 
> the temperature ?
> 
> XAvier
> 
> 
> _______________________________________________
> 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.
> 
> ------=_NextPart_000_000C_01C418FC.4459D660
> Content-Type: application/octet-stream;
> 	name="md.mdp"
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: attachment;
> 	filename="md.mdp"
> 
> title                    =3D DWNT MD=0A=
> cpp                      =3D /lib/cpp=0A=
> include                  =3D =0A=
> define                   =3D =0A=
> =0A=
> integrator               =3D md=0A=
> tinit                    =3D 0=0A=
> dt                       =3D 0.002    ; 1 fs=0A=
> nsteps                   =3D 1000    ; 1 ps=0A=
> init_step                =3D 0=0A=
> comm_mode                =3D None=0A=
> nstcomm                  =3D 0=0A=
> comm-grps                =3D =0A=
> =0A=
> nstxout                  =3D 50=0A=
> nstvout                  =3D 50=0A=
> nstfout                  =3D 50=0A=
> nstcheckpoint            =3D 1000=0A=
> nstlog                   =3D 100=0A=
> nstenergy                =3D 100=0A=
> nstxtcout                =3D 0=0A=
> xtc_precision            =3D 1000=0A=
> xtc-grps                 =3D =0A=
> energygrps               =3D NTI NTO=0A=
> =0A=
> nstlist                  =3D 10=0A=
> ns_type                  =3D grid=0A=
> pbc                      =3D full=0A=
> rlist                    =3D 1.2=0A=
> domain-decomposition     =3D no=0A=
> =0A=
> coulombtype              =3D Cut-off=0A=
> rcoulomb-switch          =3D 0=0A=
> rcoulomb                 =3D 1.2=0A=
> ; Method for doing Van der Waals=0A=
> vdw-type                 =3D Switch=0A=
> rvdw-switch              =3D 0.2=0A=
> rvdw                     =3D 1.0=0A=
> =0A=
> ; GENERATE VELOCITIES FOR STARTUP RUN=0A=
> gen-vel                  =3D yes=0A=
> gen-temp                 =3D 500=0A=
> gen-seed                 =3D 173529=0A=
> =0A=
> ;energygrp_excl           =3D NTI NTI NTO NTO=0A=
> 
> ------=_NextPart_000_000C_01C418FC.4459D660--
> 
> 
> --__--__--
> 
> Message: 6
> Date: Thu, 01 Apr 2004 16:01:55 +0200
> From: Xavier Periole <x.periole at chem.rug.nl>
> To: gmx-users at gromacs.org
> Subject: Re: FW: [gmx-users] About  Temperature Calculation
> Reply-To: gmx-users at gromacs.org
> 
> Ane Xu wrote:
> 
> >Dear XAvier:
> >
> >    No solvent, no temperature coupling,
> >
> No solvent: not good for a good control of temperature.
> No temperature coupling: you need a equilibration periode 
> where you actually control the temperature till it reaches 
> the value you want. In NVE the E=Epot+Ecin, the equilibration 
> in needed for the equipartition of the Epot and the Ecin that 
> will (in theory) be conserved for the rest of the simulation.
> What is happening is that the Ecin you give to the system is 
> transformed into Epot and this will be as long as the 
> equipartition is not reached at the temperature you want.
> I would try Stochastic Dynamics. It is probably the best for 
> what you (I presume) want to do.
> 
> >just a NVE simulation with
> >gen_temp=300. 
> >
> in your file you have gen_temp = 500  !!! That explains why 
> you have a initial temperature of 500 K
> 
> >    Thanks.
> >    BTW: why can not I reply the mail with attachment?
> >  
> >
> I got the attachment !
> 
> XAvier
> 
> --
> ----------------------------------------------
> 
>    Xavier Periole - Ph.D.
> 
>    Dept. of Biophysical Chemistry / MD Group 
>    Univ. of Groningen
>    9747 AG Groningen
>    The Netherlands
> 
>    Tel: +31-503634329
>    Fax: +31-503634800
>    email: x.periole at chem.rug.nl
>    web-page: md.chem.rug.nl/~periole
>    
> ----------------------------------------------
> 
> 
> 
> --__--__--
> 
> Message: 7
> From: "Ane Xu" <xzp02 at mails.tsinghua.edu.cn>
> To: <gmx-users at gromacs.org>
> Subject: RE:  [gmx-users] About  Temperature Calculation
> Date: Fri, 2 Apr 2004 22:19:11 +0800
> Reply-To: gmx-users at gromacs.org
> 
> Dear Xavier:
> >    No solvent, no temperature coupling,
> >
> No solvent: not good for a good control of temperature.
> No temperature coupling: you need a equilibration periode 
> where you actually control the temperature till it reaches 
> the value you want. In NVE the E=Epot+Ecin, the equilibration 
> in needed for the equipartition of the Epot and the Ecin that 
> will (in theory) be conserved for the rest of the simulation. 
> What is happening is that the Ecin you give to the system is 
> transformed into Epot and this will be as long as the 
> equipartition is not reached at the temperature you want.
> I would try Stochastic Dynamics. It is probably the best for 
> what you (I
> presume) want to do.
>      So, the 0K equilibrium potential (what I got from "em") 
> is not the "quilibrium" one in the 300K or 500K case, and if 
> I wanna got a system at 300K, the only way is to do "SD" or 
> "MD" with higher initial temperature (which results in a 
> equilibrium 300K state). Is it right?
> >just a NVE simulation with
> >gen_temp=300.
> in your file you have gen_temp = 500  !!! That explains why 
> you have a initial temperature of 500 K
>          
>     I test a case of 500K (which results in 250K finally) 
> after 300K, I forgot to explain, I am sorry for that.
> 
>     Thanks.
> 
> Ane
> 
> 
> --__--__--
> 
> Message: 8
> Date: Thu, 01 Apr 2004 16:38:42 +0200
> From: Xavier Periole <x.periole at chem.rug.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] About  Temperature Calculation
> Reply-To: gmx-users at gromacs.org
> 
> Ane Xu wrote:
> 
> >     So, the 0K equilibrium potential (what I got from "em") 
> is not the 
> >"quilibrium" one in the 300K or 500K case,
> >
> Minimization is without temperature. So no, after 
> minimization the Epot is not at all the "one" you would 
> expect to be at 300K or 500K. Note that Epot at 300 and 500 
> would be very different.
> 
> >and if I wanna got a system
> >at 300K, the only way is to do "SD" or "MD" with higher initial 
> >temperature (which results in a equilibrium 300K state). Is it right?
> >
> SD is a way to get rid of artefact due to the absence of 
> solvent. I am not a specialist of it but it seems to work well.
> Give a higher temperature to reach the one you want is not 
> the best solution. The energy you would give would be too 
> high. In general you do it in several steps where the system 
> got a chance to "relax" at each temperature: 0, 50, 100, 150, 
> 200, 250, 300 K for ex. But in vacuum will not work very good.
> 
> SD seems a better solution.
> 
> XAvier
> 
> --
> ----------------------------------------------
> 
>    Xavier Periole - Ph.D.
> 
>    Dept. of Biophysical Chemistry / MD Group 
>    Univ. of Groningen
>    9747 AG Groningen
>    The Netherlands
> 
>    Tel: +31-503634329
>    Fax: +31-503634800
>    email: x.periole at chem.rug.nl
>    web-page: md.chem.rug.nl/~periole
>    
> ----------------------------------------------
> 
> 
> 
> --__--__--
> 
> Message: 9
> Subject: RE:  [gmx-users] About  Temperature Calculation
> From: David <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Date: Thu, 01 Apr 2004 15:53:20 +0200
> Reply-To: gmx-users at gromacs.org
> 
> On Fri, 2004-04-02 at 16:19, Ane Xu wrote:
> 
> >      So, the 0K equilibrium potential (what I got from "em") is not 
> > the "quilibrium" one in the 300K or 500K case, and if I wanna got a 
> > system at 300K, the only way is to do "SD" or "MD" with 
> higher initial 
> > temperature (which results in a equilibrium 300K state). Is 
> it right?
> > >just a NVE simulation with
> > >gen_temp=300.
> > in your file you have gen_temp = 500  !!! That explains why 
> you have a 
> > initial temperature of 500 K
> >          
> 
> It could be that grompp estimates the number of degrees of 
> freedom incorrectly. Please check the number. If you have a 
> CNT in principle every carbon has three bonds.  If you use 
> constraints that will mean that each carbon has 1.5 (3 - 
> 3*0.5) degrees of freedom. If you do not use constraints it 
> should simply be 3 per carbon.
> 
> 
> >     I test a case of 500K (which results in 250K finally) 
> after 300K, 
> > I forgot to explain, I am sorry for that.
> > 
> >     Thanks.
> > 
> > Ane
> > 
> > _______________________________________________
> > 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.
> --
> David.
> ______________________________________________________________
> __________
> David van der Spoel, PhD, Assist. 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
> 
> 
> --__--__--
> 
> Message: 10
> Date: Thu, 1 Apr 2004 09:12:51 -0800 (PST)
> From: xiaobing tian <xiaobingtian at yahoo.com>
> Subject: Re: [gmx-users] left-hand warnings?
> To: gmx-users at gromacs.org
> Reply-To: gmx-users at gromacs.org
> 
> --0-333488782-1080839571=:87010
> Content-Type: text/plain; charset=us-ascii
> Content-Id: 
> Content-Disposition: inline
> 
> Dear gmx users,
> 
> When I prepared Position-restrained MD, grompp
> generated a Warning:Unknown left-hand warnings in
> parameter file.
> What does this mean? (I attached my pr.mdp file.)
> 
> Thank you very much in advance.
> 
> Xiaobing
> 
> =====
> Xiaobing Tian  Ph.D.
> Department of Microbiology and Immunology
> Thomas Jefferson University
> 1025 Walnut St., Suite 420
> Philadelphia,  PA19107
> Phone: 215-955-1364 (Lab)
> 
> __________________________________
> Do you Yahoo!?
> Yahoo! Small Business $15K Web Design Giveaway 
> http://promotions.yahoo.com/design_giveaway/
> --0-333488782-1080839571=:87010
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> Content-Transfer-Encoding: base64
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> --0-333488782-1080839571=:87010--
> 
> --__--__--
> 
> Message: 11
> Subject: Re: [gmx-users] left-hand warnings?
> From: David <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Date: Thu, 01 Apr 2004 18:28:48 +0200
> Reply-To: gmx-users at gromacs.org
> 
> On Thu, 2004-04-01 at 19:12, xiaobing tian wrote:
> > Dear gmx users,
> > 
> > When I prepared Position-restrained MD, grompp
> > generated a Warning:Unknown left-hand warnings in
> > parameter file.
> > What does this mean? (I attached my pr.mdp file.)
> 
> What it says: there is no variable 'warnings' anymore (now a command
> line option for grompp). This is harmless though.
> 
> > 
> > Thank you very much in advance.
> > 
> > Xiaobing
> > 
> > =====
> > Xiaobing Tian  Ph.D.
> > Department of Microbiology and Immunology
> > Thomas Jefferson University
> > 1025 Walnut St., Suite 420
> > Philadelphia,  PA19107
> > Phone: 215-955-1364 (Lab)
> > 
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! Small Business $15K Web Design Giveaway 
> > http://promotions.yahoo.com/design_giveaway/
> -- 
> David.
> ______________________________________________________________
> __________
> David van der Spoel, PhD, Assist. 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++
> 
> 
> --__--__--
> 
> Message: 12
> From: "Itamar Kass" <ikass at cc.huji.ac.il>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Trajectory to .pdb
> Date: Thu, 1 Apr 2004 19:36:47 +0200
> Organization: The Hrbre University, Jersualem, Israel.
> Reply-To: gmx-users at gromacs.org
> 
>   If you want to convert to pdb only the last frame at the 
> trr file you can
> use the -e flage and the last time step.
> ----- Original Message ----- 
> From: "Peter Zoon" <zoon at science.uva.nl>
> To: <gmx-users at gromacs.org>
> Sent: Thursday, April 01, 2004 3:44 PM
> Subject: Re: [gmx-users] Trajectory to .pdb
> 
> 
> > You could do that with trjconv, and then export evry frame to pdb.
> > Keep in mind that the fileszie will increase dramatically !
> > If its only 1 structure it doesn't matter, but if you want 
> to convert
> > the whole trajectory I couldn't see why you would want to do that.
> >
> > Cheers
> > Peter
> >
> > >Dear Gromacs Users,
> > >I have the run the simulation of protein in water and now I want to
> > >convert the final trajectory file(.trr) to .pdb file. 
> Please guide me how
> > >can I do that?
> > >
> > >Sincerely
> > >Ankur
> > >
> >
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> 
> 
> 
> --__--__--
> 
> Message: 13
> Date: Thu, 01 Apr 2004 20:59:19 +0000
> From: Dallas Warren <Dallas.Warren at vcp.monash.edu.au>
> Subject: Re: [gmx-users] Force Fields and Electrostatics
> To: gmx-users at gromacs.org
> Reply-To: gmx-users at gromacs.org
> 
> David,
> 
> Thank you for the reply, much appreciated.
> 
> Is there anyone else out there that had simulated the same 
> system using different treatment of the electrostatics?  And 
> find a difference, or not?
> 
> Catch ya,
> Dallas Warren
> 
> 
> --__--__--
> 
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