[gmx-users] installation probem on Tru64 supercomputer

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Thu Jan 8 10:47:01 CET 2004


Dear Wei Fu,
I also use Tru64 supercomputer here, it works quite well.
Here I send my configuration options:

./configure --enable-mpi --prefix=**  --disable-float  --enable-vector

hope it helps you
Regards
Yuguang
 
Dr. Yuguang Mu
Division of Computational and Structrual Biology
School of Biological Sciences
Nanyang Technological University
Singapore 637820
Tel: 0065-67906489
Mail: ygmu at ntu.edu.sg

-----Original Message-----
From: Wei Fu [mailto:fuwei at adrik.bchs.uh.edu] 
Sent: Thursday, January 08, 2004 5:45 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] installation probem on Tru64 supercomputer

Dear users,

    I have installed gromacs on tru64 supercomputer (Compaq, alpha-ev68), there is some abnomal installation problem (like Making all in man1
No suffix list.), but all commands seem to work after finishing installation. When I submit job by using qsub (I calculate at lemieux mathine, and use prun instead of mpirun to submit paralell job), the MD is terminated before it begins to run. No error infomation, the md.log is finished with:

*****************************************************
starting mdrun 'Protein in water'
20000 steps,     40.0 ps.


Back Off! I just backed up 3.trr to ./#3.trr.1#
*****************************************************

    I check the ener.edr and traj.trr file, it did not begin to run MD at all.

    Does anybody have experience on the installation or calculation of GROMACS on Tru64 supercomputer? Any suggestion is appreciated!

Happy new year!

Fu, Wei
2004-01-07

************************************************************
  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry 
  University of Houston
  4800 Calhoun Rd. HSC #402C
  Houston, TX 77204-5001   USA
  Phone:713-743-8355(o)  713-795-9270(h) 
  Fax:713-743-8351 
  Email: fuwei at adrik.bchs.uh.edu
  http://adrik.bchs.uh.edu/~fuwei/
  http://uh.edu
**************************************************************

======= At 2004-01-07, 22:08:00 you wrote: =======

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>Today's Topics:
>
>   1. Re: Is there an easy way to disable the choice prompt in g_rmsf? (Marc Baaden)
>   2. Re: ngmx (Osmany Guirola Cruz)
>   3. Re: ngmx (David van der Spoel)
>   4. Is there an easy way to disable the choice prompt in g_rmsf? (Berk Hess)
>   5. Re: ngmx (Nuno R. L. Ferreira)
>   6. Re: gmx-users digest, Vol 1 #1190 - NVE problems (Anton) (istvan at kolossvary.hu)
>   7. cutt offs (Ilya Chorny)
>   8. Re: cutt offs (David)
>   9. RE: cutt offs (Ilya Chorny)
>  10. RE: cutt offs (David)
>
>--__--__--
>
>Message: 1
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Is there an easy way to disable the choice prompt in g_rmsf? 
>Date: Wed, 07 Jan 2004 16:37:08 +0100
>From: Marc Baaden <baaden at smplinux.de>
>Reply-To: gmx-users at gromacs.org
>
>
>Hi Hua,
>
>this seems to become a FAQ.
>In addition to the already proposed solutions, you can also do
>
>echo -e "1\n<insert whatever you want here>" | g_rmsf ...
>
>Marc
>
>>>> Hua Wong said:
> >> Here is my problem :
> >> I have a hundred SA structures and wish to calculate de RMSF of some part 
> >> of the molecule. I want to make it automatically using a small shell 
> >> script. But how can I tell g_rmsf the choices I want whitout 
> >> the software pausing his execution to prompt me? Is there 
> >> a file I have to modify or just an option I might have misunderstood?
> >> 
> >> Thanks
> >> 
> >> -- 
> >> ----------------------------------------------------------
> >> | Wong Hua (Student)                                       |
> >> | Equipe de Bioinformatique Genomique et Moleculaire       |
> >> | INSERM U436 Universite ParisVII     _____________________|
> >> | 2 place Jussieu case 7113          | Tel:None            |
> >> | 75251 PARIS Cedex 05               | Fax:None            |
> >>  ----------------------------------------------------------
> >> 
> >> 
> >> _______________________________________________
> >> 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.
> >> 
>
>Marc Baaden
>
>-- 
> Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
> FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217
>
>
>
>--__--__--
>
>Message: 2
>From: Osmany Guirola Cruz <osmany.guirola at cigb.edu.cu>
>To: gmx-users at gromacs.org
>Date: Wed, 07 Jan 2004 10:43:05 -0500
>Subject: Re: [gmx-users] ngmx
>Reply-To: gmx-users at gromacs.org
>
>I do a grompp to my tpr file with the flag -deshuf
>and then do a trjcon to my .trr file with the deshuf.ndx
>and does not work
>
>
>On Wed, 2004-01-07 at 09:38, Nuno R. L. Ferreira wrote:
>> Hi Osmany
>>=20
>> Grompp writes an index file with flag -deshuf.
>> Then, use trjconv to deshuffle your traj.
>> Regards
>> Nuno
>>=20
>>=20
>> ######################################
>> Nuno Ricardo Santos Loureiro da Silva Ferreira
>> Departamento de Qu=C3=83=C2=ADmica
>> Faculdade de Ci=C3=83=C2=AAncias e Tecnologia
>> Universidade de Coimbra
>> 3004-535 Coimbra - Portugal
>> Fax: +351 239 827703  - www.biolchem.qui.uc.pt
>> ########################################
>> ----- Original Message -----=20
>> From: "Osmany Guirola Cruz" <osmany.guirola at cigb.edu.cu>
>> To: <gmx-users at gromacs.org>
>> Sent: Wednesday, January 07, 2004 2:07 PM
>> Subject: RE: [gmx-users] ngmx
>>=20
>>=20
>> > yes i am using shuffling in my simulation in my cluster i am usin 8
>> > machines .
>> > What can i do to see my simualtion .?
>> > eliminate the shuffling option?
>> > or exist another way to see the simulation
>> >
>> >
>> >
>> > On Wed, 2004-01-07 at 08:46, David van der Spoel wrote:
>> > > On Wed, 2004-01-07 at 14:23, Osmany Guirola Cruz wrote:
>> > > > First I load my .gro file whitout problem but when I load the .trr
>> file
>> > > > to see the simulation
>> > > > VMD begins to draw my protein very bad ... It joins atoms that are =
>not
>> > > > joined before load the trr file.
>> > > > These ocurrs in many of the atoms of my system
>> > > >
>> > > does your trr file correspond to the gro file, i.e. is the order of
>> > > atoms the same?
>> > > It will not be the same when you have used shuffling for your simulat=
>ion
>> > > (on parallel computer)
>> > >
>> > > >
>> > > > -----Original Message-----
>> > > > From: David [mailto:spoel at xray.bmc.uu.se]
>> > > > Sent: Tuesday, January 06, 2004 3:53 AM
>> > > > To: gmx-users at gromacs.org
>> > > > Subject: Re: [gmx-users] ngmx
>> > > >
>> > > >
>> > > > On Mon, 2004-01-05 at 16:44, Osmany Guirola Cruz wrote:
>> > > > > I need to know if exist another tool to visualizate
>> > > > > Trr files I think that ngmx is not the best. I use VMD but it giv=
>e
>> me
>> > > > > errors drawing  my molecules whith the trajectorie files  , I nee=
>d
>> use
>> > > >
>> > > > > other tool.
>> > > >
>> > > > What kind of errors, VMD works reasonably well for most gromacs
>> users...
>> > > >
>> > > > >   WHICH?
>> > > > >
>> > > > > _______________________________________________
>> > > > > 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.
>> >
>> >
>> > _______________________________________________
>> > 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.
>> >
>> >
>>=20
>>=20
>> _______________________________________________
>> 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=20
>> www interface or send it to gmx-users-request at gromacs.org.
>>=20
>
>
>
>--__--__--
>
>Message: 3
>Subject: Re: [gmx-users] ngmx
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>To: gmx-users at gromacs.org
>Organization: 
>Date: 07 Jan 2004 16:44:23 +0100
>Reply-To: gmx-users at gromacs.org
>
>On Wed, 2004-01-07 at 16:43, Osmany Guirola Cruz wrote:
>> I do a grompp to my tpr file with the flag -deshuf
>> and then do a trjcon to my .trr file with the deshuf.ndx
>> and does not work
>
>check the archives for deshuffling. it's a pain I'm sorry to say, but it
>can be done.
>
>>=20
>>=20
>> On Wed, 2004-01-07 at 09:38, Nuno R. L. Ferreira wrote:
>> > Hi Osmany
>> >=20
>> > Grompp writes an index file with flag -deshuf.
>> > Then, use trjconv to deshuffle your traj.
>> > Regards
>> > Nuno
>> >=20
>> >=20
>> > ######################################
>> > Nuno Ricardo Santos Loureiro da Silva Ferreira
>> > Departamento de Qu=C3=C2=ADmica
>> > Faculdade de Ci=C3=C2=AAncias e Tecnologia
>> > Universidade de Coimbra
>> > 3004-535 Coimbra - Portugal
>> > Fax: +351 239 827703  - www.biolchem.qui.uc.pt
>> > ########################################
>> > ----- Original Message -----=20
>> > From: "Osmany Guirola Cruz" <osmany.guirola at cigb.edu.cu>
>> > To: <gmx-users at gromacs.org>
>> > Sent: Wednesday, January 07, 2004 2:07 PM
>> > Subject: RE: [gmx-users] ngmx
>> >=20
>> >=20
>> > > yes i am using shuffling in my simulation in my cluster i am usin 8
>> > > machines .
>> > > What can i do to see my simualtion .?
>> > > eliminate the shuffling option?
>> > > or exist another way to see the simulation
>> > >
>> > >
>> > >
>> > > On Wed, 2004-01-07 at 08:46, David van der Spoel wrote:
>> > > > On Wed, 2004-01-07 at 14:23, Osmany Guirola Cruz wrote:
>> > > > > First I load my .gro file whitout problem but when I load the .=
>trr
>> > file
>> > > > > to see the simulation
>> > > > > VMD begins to draw my protein very bad ... It joins atoms that =
>are not
>> > > > > joined before load the trr file.
>> > > > > These ocurrs in many of the atoms of my system
>> > > > >
>> > > > does your trr file correspond to the gro file, i.e. is the order =
>of
>> > > > atoms the same?
>> > > > It will not be the same when you have used shuffling for your sim=
>ulation
>> > > > (on parallel computer)
>> > > >
>> > > > >
>> > > > > -----Original Message-----
>> > > > > From: David [mailto:spoel at xray.bmc.uu.se]
>> > > > > Sent: Tuesday, January 06, 2004 3:53 AM
>> > > > > To: gmx-users at gromacs.org
>> > > > > Subject: Re: [gmx-users] ngmx
>> > > > >
>> > > > >
>> > > > > On Mon, 2004-01-05 at 16:44, Osmany Guirola Cruz wrote:
>> > > > > > I need to know if exist another tool to visualizate
>> > > > > > Trr files I think that ngmx is not the best. I use VMD but it=
> give
>> > me
>> > > > > > errors drawing  my molecules whith the trajectorie files  , I=
> need
>> > use
>> > > > >
>> > > > > > other tool.
>> > > > >
>> > > > > What kind of errors, VMD works reasonably well for most gromacs
>> > users...
>> > > > >
>> > > > > >   WHICH?
>> > > > > >
>> > > > > > _______________________________________________
>> > > > > > 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.
>> > >
>> > >
>> > > _______________________________________________
>> > > 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.
>> > >
>> > >
>> >=20
>> >=20
>> > _______________________________________________
>> > 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=20
>> > www interface or send it to gmx-users-request at gromacs.org.
>> >=20
>>=20
>>=20
>> _______________________________________________
>> 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=20
>> www interface or send it to gmx-users-request at gromacs.org.
>--=20
>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: 4
>From: "Berk Hess" <gmx3 at hotmail.com>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Is there an easy way to disable the choice prompt in g_rmsf?
>Date: Wed, 07 Jan 2004 16:55:48 +0100
>Reply-To: gmx-users at gromacs.org
>
>Hi,
>
>Yet another solution:
>You can make an index file which contains only one group,
>the one you want to analyze. In that case g_rmsf and many other
>Gromacs programs will not prompt you for group selection.
>
>Berk.
>
>
>Hua Wong wrote:
>
>>Here is my problem :
>>I have a hundred SA structures and wish to calculate de RMSF of some part 
>>of the molecule. I want to make it automatically using a small shell 
>>script. But how can I tell g_rmsf the choices I want whitout the software 
>>pausing his execution to prompt me? Is there a file I have to modify or 
>>just an option I might have misunderstood?
>>
>>Thanks
>>
>
>_________________________________________________________________
>Play online games with your friends with MSN Messenger 
>http://messenger.msn.nl/
>
>
>--__--__--
>
>Message: 5
>From: "Nuno R. L. Ferreira" <nunolf at ci.uc.pt>
>To: <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] ngmx
>Date: Wed, 7 Jan 2004 15:53:30 -0000
>Reply-To: gmx-users at gromacs.org
>
>What about your pbc treatment? Try -pbc whole with -n reading your deshuffle
>index file.
>And, check e-mail .
>NUno
>
>
>######################################
>Nuno Ricardo Santos Loureiro da Silva Ferreira
>Departamento de Química
>Faculdade de Ciências e Tecnologia
>Universidade de Coimbra
>3004-535 Coimbra - Portugal
>Fax: +351 239 827703  - www.biolchem.qui.uc.pt
>########################################
>----- Original Message ----- 
>From: "Osmany Guirola Cruz" <osmany.guirola at cigb.edu.cu>
>To: <gmx-users at gromacs.org>
>Sent: Wednesday, January 07, 2004 3:43 PM
>Subject: Re: [gmx-users] ngmx
>
>
>I do a grompp to my tpr file with the flag -deshuf
>and then do a trjcon to my .trr file with the deshuf.ndx
>and does not work
>
>
>On Wed, 2004-01-07 at 09:38, Nuno R. L. Ferreira wrote:
>> Hi Osmany
>>
>> Grompp writes an index file with flag -deshuf.
>> Then, use trjconv to deshuffle your traj.
>> Regards
>> Nuno
>>
>>
>> ######################################
>> Nuno Ricardo Santos Loureiro da Silva Ferreira
>> Departamento de QuÃf­mica
>> Faculdade de CiÃfªncias e Tecnologia
>> Universidade de Coimbra
>> 3004-535 Coimbra - Portugal
>> Fax: +351 239 827703  - www.biolchem.qui.uc.pt
>> ########################################
>> ----- Original Message ----- 
>> From: "Osmany Guirola Cruz" <osmany.guirola at cigb.edu.cu>
>> To: <gmx-users at gromacs.org>
>> Sent: Wednesday, January 07, 2004 2:07 PM
>> Subject: RE: [gmx-users] ngmx
>>
>>
>> > yes i am using shuffling in my simulation in my cluster i am usin 8
>> > machines .
>> > What can i do to see my simualtion .?
>> > eliminate the shuffling option?
>> > or exist another way to see the simulation
>> >
>> >
>> >
>> > On Wed, 2004-01-07 at 08:46, David van der Spoel wrote:
>> > > On Wed, 2004-01-07 at 14:23, Osmany Guirola Cruz wrote:
>> > > > First I load my .gro file whitout problem but when I load the .trr
>> file
>> > > > to see the simulation
>> > > > VMD begins to draw my protein very bad ... It joins atoms that are
>not
>> > > > joined before load the trr file.
>> > > > These ocurrs in many of the atoms of my system
>> > > >
>> > > does your trr file correspond to the gro file, i.e. is the order of
>> > > atoms the same?
>> > > It will not be the same when you have used shuffling for your
>simulation
>> > > (on parallel computer)
>> > >
>> > > >
>> > > > -----Original Message-----
>> > > > From: David [mailto:spoel at xray.bmc.uu.se]
>> > > > Sent: Tuesday, January 06, 2004 3:53 AM
>> > > > To: gmx-users at gromacs.org
>> > > > Subject: Re: [gmx-users] ngmx
>> > > >
>> > > >
>> > > > On Mon, 2004-01-05 at 16:44, Osmany Guirola Cruz wrote:
>> > > > > I need to know if exist another tool to visualizate
>> > > > > Trr files I think that ngmx is not the best. I use VMD but it give
>> me
>> > > > > errors drawing  my molecules whith the trajectorie files  , I need
>> use
>> > > >
>> > > > > other tool.
>> > > >
>> > > > What kind of errors, VMD works reasonably well for most gromacs
>> users...
>> > > >
>> > > > >   WHICH?
>> > > > >
>> > > > > _______________________________________________
>> > > > > 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.
>> >
>> >
>> > _______________________________________________
>> > 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.
>> >
>> >
>>
>>
>> _______________________________________________
>> 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.
>>
>
>
>_______________________________________________
>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.
>
>
>
>
>--__--__--
>
>Message: 6
>From: istvan at kolossvary.hu
>To: gmx-users at gromacs.org
>Date: Wed, 07 Jan 2004 17:01:30 +0100
>Subject: [gmx-users] Re: gmx-users digest, Vol 1 #1190 - NVE problems (Anton)
>Reply-To: gmx-users at gromacs.org
>
>Anton, 
>
>Your drift with SPC box sounds pretty good to me, mine current drift is 
>several kJ/mol/ps. Was that single or double precision? I'll try to run it 
>in double precision. 
>
>Thanks, 
>
>  Istvan
>
>--__--__--
>
>Message: 7
>From: "Ilya Chorny" <ichorny at maxwell.compbio.ucsf.edu>
>To: <gmx-users at gromacs.org>
>Date: Wed, 7 Jan 2004 12:45:23 -0800
>Subject: [gmx-users] cutt offs
>Reply-To: gmx-users at gromacs.org
>
>I ran a whole new set of calculations calculating the solvation of
>molecules in SPC. I get significantly different results if I use a
>cutoff distance of 1.4 for the LJ vs .8. I always assumed that the LJ
>interaction falls off much faster than that but I guess I was ignoring
>the Jacobian. Do other people see this kind of effect? The SPC water
>becomes significantly more stable with the larger cutoff distances I
>think this is where it would be useful to have a cutoff distance that is
>different for the solute then the solvent. What cutt off distances is
>SPC parameterized for?
>
>Thanks
>
>Ilya
>
>
>
>
>--__--__--
>
>Message: 8
>Subject: Re: [gmx-users] cutt offs
>From: David <spoel at xray.bmc.uu.se>
>To: gmx-users at gromacs.org
>Organization: 
>Date: 07 Jan 2004 21:00:46 +0100
>Reply-To: gmx-users at gromacs.org
>
>On Wed, 2004-01-07 at 21:45, Ilya Chorny wrote:
>> I ran a whole new set of calculations calculating the solvation of
>> molecules in SPC. I get significantly different results if I use a
>> cutoff distance of 1.4 for the LJ vs .8. I always assumed that the LJ
>> interaction falls off much faster than that but I guess I was ignoring
>> the Jacobian. Do other people see this kind of effect? The SPC water
>> becomes significantly more stable with the larger cutoff distances I
>> think this is where it would be useful to have a cutoff distance that is
>> different for the solute then the solvent. What cutt off distances is
>> SPC parameterized for?
>0.9 nm.
>
>However, the latest GROMOS proten force field is parameterized for
>twin/range 0.8/1.4 although most people probably run it with 0.9/1.4.
>(Oh, and nstlist should be 5 steps of 2 fs with shake).
>
>> Thanks
>> 
>> Ilya
>> 
>> 
>> 
>> _______________________________________________
>> 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: 9
>From: "Ilya Chorny" <ichorny at maxwell.compbio.ucsf.edu>
>To: <gmx-users at gromacs.org>
>Subject: RE: [gmx-users] cutt offs
>Date: Wed, 7 Jan 2004 12:58:07 -0800
>Reply-To: gmx-users at gromacs.org
>
>So what do I do when I have a solute that has a 1nm radius?
>
>Ilya
>
>
>-----Original Message-----
>From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
>On Behalf Of David
>Sent: Wednesday, January 07, 2004 12:01 PM
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] cutt offs
>
>On Wed, 2004-01-07 at 21:45, Ilya Chorny wrote:
>> I ran a whole new set of calculations calculating the solvation of
>> molecules in SPC. I get significantly different results if I use a
>> cutoff distance of 1.4 for the LJ vs .8. I always assumed that the LJ
>> interaction falls off much faster than that but I guess I was ignoring
>> the Jacobian. Do other people see this kind of effect? The SPC water
>> becomes significantly more stable with the larger cutoff distances I
>> think this is where it would be useful to have a cutoff distance that
>is
>> different for the solute then the solvent. What cutt off distances is
>> SPC parameterized for?
>0.9 nm.
>
>However, the latest GROMOS proten force field is parameterized for
>twin/range 0.8/1.4 although most people probably run it with 0.9/1.4.
>(Oh, and nstlist should be 5 steps of 2 fs with shake).
>
>> Thanks
>> 
>> Ilya
>> 
>> 
>> 
>> _______________________________________________
>> 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
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>_______________________________________________
>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 
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>
>
>
>--__--__--
>
>Message: 10
>Subject: RE: [gmx-users] cutt offs
>From: David <spoel at xray.bmc.uu.se>
>To: gmx-users at gromacs.org
>Organization: 
>Date: 07 Jan 2004 21:11:02 +0100
>Reply-To: gmx-users at gromacs.org
>
>On Wed, 2004-01-07 at 21:58, Ilya Chorny wrote:
>> So what do I do when I have a solute that has a 1nm radius?
>> 
>Is this still your single particle? In that case there is a problem,
>otherwise each charge group in your molecule sees every water within the
>cut-off... The twin range takes care of the long range forces. Don't
>know about long range free energy contribution... 
>
>> Ilya
>> 
>> 
>> -----Original Message-----
>> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
>> On Behalf Of David
>> Sent: Wednesday, January 07, 2004 12:01 PM
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] cutt offs
>> 
>> On Wed, 2004-01-07 at 21:45, Ilya Chorny wrote:
>> > I ran a whole new set of calculations calculating the solvation of
>> > molecules in SPC. I get significantly different results if I use a
>> > cutoff distance of 1.4 for the LJ vs .8. I always assumed that the LJ
>> > interaction falls off much faster than that but I guess I was ignoring
>> > the Jacobian. Do other people see this kind of effect? The SPC water
>> > becomes significantly more stable with the larger cutoff distances I
>> > think this is where it would be useful to have a cutoff distance that
>> is
>> > different for the solute then the solvent. What cutt off distances is
>> > SPC parameterized for?
>> 0.9 nm.
>> 
>> However, the latest GROMOS proten force field is parameterized for
>> twin/range 0.8/1.4 although most people probably run it with 0.9/1.4.
>> (Oh, and nstlist should be 5 steps of 2 fs with shake).
>> 
>> > Thanks
>> > 
>> > Ilya
>> > 
>> > 
>> > 
>> > _______________________________________________
>> > 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
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>--__--__--
>
>_______________________________________________
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>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
>End of gmx-users Digest


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