[gmx-users] pb with temperature in bd (2)
BON Michael
michael.bon at cea.fr
Tue Jul 3 10:04:34 CEST 2007
I just wanted to add one thing to my previous mail, that may give some insight to a skilled Gromacs user :
when I replace bd with md or sd in the .mdp, the system is correctly equilibrated with the required
temperature. This problem of doubling temperature (ie 620 instead of 310) occurs only with bd.
Thanks again,
Michael BON
-------- Message d'origine--------
De: gmx-users-bounces at gromacs.org de la part de gmx-users-request at gromacs.org
Date: mar. 03/07/2007 06:05
À: gmx-users at gromacs.org
Objet : gmx-users Digest, Vol 39, Issue 9
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Today's Topics:
1. Re: pdb2gmx not recognizing disulfides (Mark Abraham)
2. Re: which tpr? (Mark Abraham)
3. Re: [Fwd: How simulate two peptides in a box?] (Mark Abraham)
4. Re: Applying constant force between two atoms (SeungPyo Hong )
5. g_wham and PMF problem (Sudha Mani Karra)
6. Re: g_wham and PMF problem (Mark Abraham)
7. How to get ligand top file for oplsaa? (Rui Li)
8. Re: which tpr? (Tsjerk Wassenaar)
----------------------------------------------------------------------
Message: 1
Date: Tue, 3 Jul 2007 11:49:09 +1000 (EST)
From: "Mark Abraham" <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] pdb2gmx not recognizing disulfides
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID: <3674.59.167.49.193.1183427349.squirrel at sqmail.anu.edu.au>
Content-Type: text/plain;charset=iso-8859-1
> Thanks for the tip. I didn't think to try it. But if I plan to do any
> electrostatics I still need the tpr file right? So I would need to produce
> a
> top file. Mark, you mentioned making the S-S bonds by hand.
You can see that trjconv doesn't really need a .tpr because trjconv -h
shows you that -s allows any structure file type as input. This is a
general GROMACS phenomenon.
>>You still won't get them bonded with this procedure... you need a .top
>>file with S-S bonds, and you get that by producing one by hand or using
>>pdb2gmx.
>
> Could you or anyone else point me in the right direction to do this?
I'm a bit hamstrung because I don't know
a) why you are trying to make S-S bonds from a structure that has sulfurs
more than 2A apart
b) where this structure came from
c) whether you have tried the second procedure I suggested in the email
you quote http://www.gromacs.org/pipermail/gmx-users/2007-July/028337.html
d) whether you have tried the other suggestion I made
http://www.gromacs.org/pipermail/gmx-users/2007-July/028356.html
Making the topology by hand requires you to read chapter five of the
manual thoroughly and then go through a working topology with the manual
at hand so that you understand all the bits. Only then could you hope to
make a S-S topology by hand, and then you'll probably run into hassles
with things breaking when you try to minimize with it. Much easier will be
c) or d) above.
Mark
------------------------------
Message: 2
Date: Tue, 3 Jul 2007 11:53:53 +1000 (EST)
From: "Mark Abraham" <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] which tpr?
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID: <3694.59.167.49.193.1183427633.squirrel at sqmail.anu.edu.au>
Content-Type: text/plain;charset=iso-8859-1
> Hello all,
>
> Because of the limitations in run time, my simulations have broken into
> three parts: one.trr, two.trr, and three.trr. Each run has its
> corresponding
> tpr file. The original tpr file (minimization step) was start.tpr. Now
> using
> trjconv for three.trr which tpr file I need to type after -s option?
>
> trjconv -f three.trr -s start.tpr ....
>
> I am aware that the topology (information in the starting top file) will
> remain intact during simulation. I am wondering whether commands like
> trjconv read anything more than topology information (MD parameters, etc)
> from the -s option? In other words, in the above example replacing
> start.tprwith
> three.tpr will not change the outcome?
trjconv just needs any old structure file. You can see this if you follow
my suggestion at the top of this post
http://www.gromacs.org/pipermail/gmx-users/2007-July/028367.html
Mark
------------------------------
Message: 3
Date: Tue, 3 Jul 2007 12:02:55 +1000 (EST)
From: "Mark Abraham" <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] [Fwd: How simulate two peptides in a box?]
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<52410.150.203.145.27.1183428175.squirrel at sqmail.anu.edu.au>
Content-Type: text/plain;charset=iso-8859-1
> Hello Gromacs users:
Please don't reply to another user's question with a change of topic and
not change the subject line of your email. Not doing this means the people
who might know the answer for you have no idea in advance what you're
going to be asking, and might not bother reading. Best is to start with a
new email, not a reply, and to use your subject line sensibly.
> I am running a dimeric protein simulation on Gromacs 3.3 using the force
> filed G43a1.
>
>
> For initially minimizing the hydrogen i did some small minimization and
> equilibration in the vacuum by maintaining the restraints
> then i added ions and water but in the very first minimization i m getting
> the following error
If you want to keep your credibility, when people have already made a
suggestion about how to solve your problem, such as I did here
http://www.gromacs.org/pipermail/gmx-users/2007-June/028301.html, when you
post the same problem, you should say what happened when you tried their
suggestion. They didn't suggest it for their own entertainment.
Look at the minimization "trajectory" and see where things are breaking.
Have a look at your topology there, read chapter five thoroughly.
Mark
------------------------------
Message: 4
Date: Tue, 3 Jul 2007 11:01:48 +0900
From: "SeungPyo Hong " <sp1020 at gmail.com>
Subject: Re: [gmx-users] Applying constant force between two atoms
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<bd5475eb0707021901j70760445p6b29538db78372ec at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Thank you for paying attention.
Maybe I have to study much more about Gromacs. ^^;
Seungpyo
On 7/2/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
>
> > Dear gmx-users,
> >
> >
> >
> > I want to apply constant force between two atoms within a protein.
> >
> > But unfortunately I cannot find how to apply constant force.
> >
> > Would anybody talk me how to do it?
>
> Probably not, but if you read Chapters 3-5 of the manual, you will see
> some ideas that are probably more suitable for whatever your underlying
> objective is.
>
> Mark
>
> _______________________________________________
> 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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>
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Message: 5
Date: Mon, 2 Jul 2007 22:32:51 -0500
From: "Sudha Mani Karra" <karra.md at gmail.com>
Subject: [gmx-users] g_wham and PMF problem
To: gmx-users at gromacs.org
Message-ID:
<c9c53acb0707022032h50b00c1p77c2bec9545ea335 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hey All,
I am trying to use g_wham command to compute PMF.Can anyone please let
me know how to use that command?
When I try giving the input files sequentially like
g_wham -o PMF.XVG -hist pull1.pdo pull2.pdo pull3.pdo,
there is an error message saying, that it is not a valid input file format.
I have seen in the previous mailing lists that people have faced the same
kind of error. I hope I get a reply from them as they would have solved
this.
Thanks in advance.
S.Karra.
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Message: 6
Date: Tue, 3 Jul 2007 13:49:55 +1000 (EST)
From: "Mark Abraham" <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] g_wham and PMF problem
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<36211.150.203.145.27.1183434595.squirrel at sqmail.anu.edu.au>
Content-Type: text/plain;charset=iso-8859-1
> Hey All,
> I am trying to use g_wham command to compute PMF.Can anyone please let
> me know how to use that command?
Well there's g_wham -h and the section on WHAMin the manual...
> When I try giving the input files sequentially like
>
> g_wham -o PMF.XVG -hist pull1.pdo pull2.pdo pull3.pdo,
>
> there is an error message saying, that it is not a valid input file
> format.
Please be specific about the error message and the file that caused it.
Computers are precise, and you should be also in describing their
responses to your inputs.
Mark
------------------------------
Message: 7
Date: Tue, 03 Jul 2007 11:58:30 +0800
From: "Rui Li" <moonfine at mail.sdu.edu.cn>
Subject: [gmx-users] How to get ligand top file for oplsaa?
To: gmx-users at gromacs.org
Message-ID: <383435110.29013 at mail.sdu.edu.cn>
Content-Type: text/plain
Dear all,
I have a ligand molecule, and I want to get its opls all-atom force field topology
file. How can I get it?
I don't know how to establish the atom types and the charge of the ligand.
Any reply will be appreciated.
sincerely
Rui Li
------------------------------
Message: 8
Date: Tue, 3 Jul 2007 06:05:34 +0200
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Subject: Re: [gmx-users] which tpr?
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<8ff898150707022105r7b099c2ega875615c72d7b9d0 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hey :)
Errm, trjconv does read coordinates, so when using -fit or -pbc
nojump, the results will depend on the structure file used.
Tsjerk
On 7/3/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > Hello all,
> >
> > Because of the limitations in run time, my simulations have broken into
> > three parts: one.trr, two.trr, and three.trr. Each run has its
> > corresponding
> > tpr file. The original tpr file (minimization step) was start.tpr. Now
> > using
> > trjconv for three.trr which tpr file I need to type after -s option?
> >
> > trjconv -f three.trr -s start.tpr ....
> >
> > I am aware that the topology (information in the starting top file) will
> > remain intact during simulation. I am wondering whether commands like
> > trjconv read anything more than topology information (MD parameters, etc)
> > from the -s option? In other words, in the above example replacing
> > start.tprwith
> > three.tpr will not change the outcome?
>
> trjconv just needs any old structure file. You can see this if you follow
> my suggestion at the top of this post
> http://www.gromacs.org/pipermail/gmx-users/2007-July/028367.html
>
> Mark
>
> _______________________________________________
> 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!
> 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
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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