[gmx-users] neutral LYS (NH2)
mauricio arenas
marenas at usach.cl
Wed Jul 28 10:57:12 CEST 2004
I need to know since I can make a MD of a neutral LYS (NH2).
thank you very much
Mauricio Arenas Salinas
Centro de Bioinformatica
Universidad de Talca
Fono: 56-71-201661
Fax : 56-71-201561
marenas at utalca.cl
Talca,Chile.
-------Mensaje original-------
De: gmx-users at gromacs.org
Fecha: 07/27/04 14:44:54
Para: gmx-users at gromacs.org
Asunto: gmx-users Digest, Vol 3, Issue 65
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Today's Topics:
1. Re: The meaning of rlist, rvdm and rcolumn (Anton Feenstra)
2. CRY-ED question (Ruben Martinez Buey)
3. Re: CRY-ED question (Bert de Groot)
4. multiple backups (Berk Hess)
5. Re: multiple backups (Nguyen Hoang Phuong)
6. Re: problem with -multi (Anton Feenstra)
7. Re: multiple backups (Bert de Groot)
8. Re: multiple backups (Andrey V Golovin)
9. Re: multiple backups (Anton Feenstra)
----------------------------------------------------------------------
Message: 1
Date: Tue, 27 Jul 2004 13:38:57 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] The meaning of rlist, rvdm and rcolumn
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <41063ED1.3030709 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed
Li Dawei wrote:
> 1, In every nstlist steps, neighbor will be build. And the neighbor list
> contains pairs whose distance is shorter than rvdw or rcoul.
> 2, Only paris whose distance is shorter than rlist will be calculated in
> each step?
>
> If this is the case, the actual cut-off is rlist?
No. Forces for distances up to rvdw and rcoul are evaluated each
nstlist steps, and these forces are used till the next update (nstlist
steps later). Forces for distanes < rlist are evaluated each step.
> Am I rihgt? Another problem is that grompp still report that rlist>rvdm
> is an error even vmdtypw is set to shift.
I wouldn't be surprized if the manual and the code for shift disagree...
IIRC, this has been discussed before on the list, have you searched for
this?
--
Groetjes,
Anton
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
|_____________|_______________________________________________________|
------------------------------
Message: 2
Date: Tue, 27 Jul 2004 13:40:31 +0200
From: Ruben Martinez Buey <ruben at akilonia.cib.csic.es>
Subject: [gmx-users] CRY-ED question
To: gmx-users at gromacs.org
Message-ID: <41063F2F.67830C3C at akilonia.cib.csic.es>
Content-Type: text/plain; charset="iso-8859-1"
> Hi all,
I would like to compare my MD/ED simulations with a CRY-ED analysis of my
protein,
but I only have two crystal structures. Can I correctly deduce the essential
dynamics from only two experimental conformations?
Thanks a lot in advance,
Bests,
Ruben
--
___________________________________________
Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144, 28006 MADRID (SPAIN)
Tlf: +34-91-561 18 00 ext. 4380
Fax: +34-91-562 75 18
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Message: 3
Date: Tue, 27 Jul 2004 14:01:29 +0200
From: Bert de Groot <bgroot at gwdg.de>
Subject: Re: [gmx-users] CRY-ED question
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <41064419.3090003 at gwdg.de>
Content-Type: text/plain; charset=us-ascii; format=flowed
Ruben Martinez Buey wrote:
>> Hi all,
>
> I would like to compare my MD/ED simulations with a CRY-ED analysis of
> my protein, but I only have two crystal structures. Can I correctly
> deduce the essential dynamics from only two experimental conformations?
>
Only partially. Obviously, from a PCA in this case you'll get only one
(meaningful) eigenvector:
the difference vector between the two conformations.
But this can still be used in e.g. a comparison to a simulation.
Bert
____________________________________________________________________________
Dr. Bert de Groot
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany
tel: +49-551-2012308, fax: +49-551-2012302
email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________
------------------------------
Message: 4
Date: Tue, 27 Jul 2004 14:09:41 +0200
From: "Berk Hess" <gmx3 at hotmail.com>
Subject: [gmx-users] multiple backups
To: gmx-users at gromacs.org
Message-ID: <BAY16-F27jSiLud7Fay000c1620 at hotmail.com>
Content-Type: text/plain; format=flowed
Hi,
I would like to know what the Gromacs users think of multiple backups.
As of version 3.1.2 Gromacs makes multiple backups of files.
If you use the same mdrun command four times
in the same directory you would have for instance:
#md.log.1#
#md.log.2#
#md.log.3#
md.log
Before version 3.1.2 Gromacs would make only one backup
and you would lose all the older files:
#md.log#
md.log
I can see that this could be useful in that you never loose files,
unless you type rm.
But personally I find all these files quite annoying and I know
of may people that think the same.
When doing analysis or when trying to start a simulation which
has some problems you often type the same command many
times and the directory is quickly flooded with more than a hundred
backup files. I have never used a backup file beyond the last backup.
So I propose to go back to the old system which has only
a single backup for each file.
Berk.
_________________________________________________________________
Don’t just search. Find. Check out the new MSN Search!
http://search.msn.click-url.com/go/onm00200636ave/direct/01/
------------------------------
Message: 5
Date: Tue, 27 Jul 2004 14:21:11 +0200 (MEST)
From: Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de>
Subject: Re: [gmx-users] multiple backups
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<Pine.LNX.4.44.0407271416010.8969-100000 at marge.theochem.uni-frankfurt.de>
Content-Type: TEXT/PLAIN; charset=US-ASCII
> I would like to know what the Gromacs users think of multiple backups.
>
> As of version 3.1.2 Gromacs makes multiple backups of files.
> If you use the same mdrun command four times
> in the same directory you would have for instance:
> #md.log.1#
> #md.log.2#
> #md.log.3#
> md.log
> Before version 3.1.2 Gromacs would make only one backup
> and you would lose all the older files:
> #md.log#
> md.log
>
> I can see that this could be useful in that you never loose files,
> unless you type rm.
> But personally I find all these files quite annoying and I know
> of may people that think the same.
> When doing analysis or when trying to start a simulation which
> has some problems you often type the same command many
> times and the directory is quickly flooded with more than a hundred
> backup files. I have never used a backup file beyond the last backup.
>
> So I propose to go back to the old system which has only
> a single backup for each file.
>
> Berk.
I absolutely agree with Berk's idea.
Phuong
------------------------------
Message: 6
Date: Tue, 27 Jul 2004 13:40:07 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] problem with -multi
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <41063F17.8010406 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed
Nguyen Hoang Phuong wrote:
> What is the reason why I should *NOT* use this option for several
> normal runs ? Is it a technical problem?
There is no point. It is so much simpler to just start several independent
mdruns.
--
Groetjes,
Anton
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
|_____________|_______________________________________________________|
------------------------------
Message: 7
Date: Tue, 27 Jul 2004 14:26:06 +0200
From: Bert de Groot <bgroot at gwdg.de>
Subject: Re: [gmx-users] multiple backups
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <410649DE.3030806 at gwdg.de>
Content-Type: text/plain; charset=us-ascii; format=flowed
Berk Hess wrote:
> Hi,
>
> I would like to know what the Gromacs users think of multiple backups.
>
personally, I can live with them, but it would be nice if with e.g. an
environment variable
one could switch back to the old, one backup only, behaviour. This
environment variable
could optionally be defined in the GMXRC file. I would probably favour a
secure default value,
ie multiple backups enabled.
Bert
____________________________________________________________________________
Dr. Bert de Groot
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany
tel: +49-551-2012308, fax: +49-551-2012302
email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________
------------------------------
Message: 8
Date: Tue, 27 Jul 2004 14:30:57 +0200
From: Andrey V Golovin <golovin at genebee.msu.su>
Subject: Re: [gmx-users] multiple backups
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <28802801.20040727143057 at genebee.msu.su>
Content-Type: text/plain; charset=us-ascii
Dear Berk,
Tuesday, July 27, 2004, 2:09:41 PM, you wrote:
BH> Hi,
BH> I would like to know what the Gromacs users think of multiple backups.
BH> As of version 3.1.2 Gromacs makes multiple backups of files.
BH> If you use the same mdrun command four times
BH> in the same directory you would have for instance:
BH> #md.log.1#
BH> #md.log.2#
BH> #md.log.3#
BH> md.log
BH> Before version 3.1.2 Gromacs would make only one backup
BH> and you would lose all the older files:
BH> #md.log#
BH> md.log
BH> I can see that this could be useful in that you never loose files,
BH> unless you type rm.
BH> But personally I find all these files quite annoying and I know
BH> of may people that think the same.
BH> When doing analysis or when trying to start a simulation which
BH> has some problems you often type the same command many
BH> times and the directory is quickly flooded with more than a hundred
BH> backup files. I have never used a backup file beyond the last backup.
yes it's REALLY annoying. =)
BH> So I propose to go back to the old system which has only
BH> a single backup for each file.
may be could be better to set up some environment variable that
responsible for number of backups.
--
Best regards,
Andrey mailto:golovin at genebee.msu.su
------------------------------
Message: 9
Date: Tue, 27 Jul 2004 14:52:51 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] multiple backups
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <41065023.40909 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed
Berk Hess wrote:
> So I propose to go back to the old system which has only
> a single backup for each file.
I simply have an alias 'clean' that does something like 'rm -f #*#' which
I type as soon as my dir becomes cluttered. I did that already with the
single backups, and still do it. For me it is fine as it is now with the
multiple backups - and occasionally I have even used the older backup files.
--
Groetjes,
Anton
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
|_____________|_______________________________________________________|
------------------------------
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
End of gmx-users Digest, Vol 3, Issue 65
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