[gmx-users] Topology for ligands
Ebert Maximilian
m.ebert at umontreal.ca
Mon Sep 28 14:40:54 CEST 2015
maybe this could be a good staring point:
http://www.esi.umontreal.ca/~pelletjo/gromacs/derive01.html
On Sep 26, 2015, at 5:14 PM, Juliano Braz Carregal <julianocarregal at hotmail.com<mailto:julianocarregal at hotmail.com>> wrote:
Can someone tell me a good program/sever besides prodg ,to generate topology for organic and inorganic ligands.thanks
Em 26/09/2015 2:48 PM, gromacs.org_gmx-users-request at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-request at maillist.sys.kth.se> escreveu:
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Today's Topics:
1. bonded forces in output (Stanislav ?imko)
2. Re: bonded forces in output (Justin Lemkul)
3. Installation problem
(Parham Jabbarzadeh (Department of Biomedical Science))
4. Restart simulation after crash (Juliano Braz Carregal)
5. Re: Restart simulation after crash (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Sat, 26 Sep 2015 11:31:24 +0200
From: Stanislav ?imko <stanislav.simko at gmail.com<mailto:stanislav.simko at gmail.com>>
To: gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] bonded forces in output
Message-ID: <1443259884.25179.9.camel at gmail.com<mailto:1443259884.25179.9.camel at gmail.com>>
Content-Type: text/plain; charset="UTF-8"
Dear gromacs users,
I'm writing my code to calculate pressure from trajectory files - from
problthat em atomic positions and forces - according to virial theorem.
Currently, I'm able to calculate the same pressure when I've got only
non-bonded forces of a small system (10 atoms with charges and LJ
parameters) centered in a big (100nm cubic) box. Hopefully, my code
should work also for smaller box where atoms can see periodic images.
The problem that I'm facing right now is that I do not know how to
obtain bonded forces from the trajectory files. E.g., for single spc
water molecule gromacs gives zero forces on all atoms, even though I
assigned them different velocities.
to obtain forces I run:
gmx traj -f *.trr -s *.tpr -of forces -fp
Also, gromacs gives me non-zero virial (diagonal elements XX, YY, ZZ),
which means that there are some forces
gmx energy -f *.edr -s *.tpr ...
So I would like to ask, if there is some way how to get bonded forces
out of the trajectory... (or rerun with some runtime parameters to
force gromacs to print bonded forces)
Sincerely,
stanislav.
------------------------------
Message: 2
Date: Sat, 26 Sep 2015 12:02:48 -0400
From: Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>>
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Re: [gmx-users] bonded forces in output
Message-ID: <5606C1A8.4090106 at vt.edu<mailto:5606C1A8.4090106 at vt.edu>>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 9/26/15 5:31 AM, Stanislav ?imko wrote:
> Dear gromacs users,
> I'm writing my code to calculate pressure from trajectory files - from
> problthat em atomic positions and forces - according to virial theorem.
> Currently, I'm able to calculate the same pressure when I've got only
> non-bonded forces of a small system (10 atoms with charges and LJ
> parameters) centered in a big (100nm cubic) box. Hopefully, my code
> should work also for smaller box where atoms can see periodic images.
> The problem that I'm facing right now is that I do not know how to
> obtain bonded forces from the trajectory files. E.g., for single spc
> water molecule gromacs gives zero forces on all atoms, even though I
> assigned them different velocities.
> to obtain forces I run:
> gmx traj -f *.trr -s *.tpr -of forces -fp
> Also, gromacs gives me non-zero virial (diagonal elements XX, YY, ZZ),
> which means that there are some forces
> gmx energy -f *.edr -s *.tpr ...
> So I would like to ask, if there is some way how to get bonded forces
> out of the trajectory... (or rerun with some runtime parameters to
> force gromacs to print bonded forces)
By default, water is treated as rigid via SETTLE, so there are no bonded forces.
You can turn this off with "define = -DFLEXIBLE" in the .mdp file for the
purpose of do a re-calculation of energies and forces.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 3
Date: Sat, 26 Sep 2015 09:08:08 -0700
From: "Parham Jabbarzadeh (Department of Biomedical Science)"
<pjabbarzadeh at gmail.com<mailto:pjabbarzadeh at gmail.com>>
To: gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Installation problem
Message-ID:
<CAGq_gb8tUi4aYyEGRL3S8smKkcWjkcQ4C2-wBtDA78zD1DsNgg at mail.gmail.com<mailto:CAGq_gb8tUi4aYyEGRL3S8smKkcWjkcQ4C2-wBtDA78zD1DsNgg at mail.gmail.com>>
Content-Type: text/plain; charset=UTF-8
Dear sir
When I am installing in the build directory, I faced the folliwng error.
Can you help me? My Ubuntu version is 15.04.
Issue another request to this URL:
'https://kth.box.com/shared/static/53xl0qouhsvrbrbgtl4p.gz'
Protocol "https" not supported or disabled in libcurl
Closing connection -1
-- Configuring incomplete, errors occurred!
Thanks
*?Parham Jabbarzadeh Kaboli*=========================
??
========
?========?
Cancer Pharmacologist
Faculty of Medicine and Health Sciences
University Putra Malaysia
Malaysia
=================================
?========?
Publication <http://www.ncbi.nlm.nih.gov/pubmed/?term=Parham+Jabbarzadeh+Kaboli>:::
Featured Publication
<http://www.sciencedirect.com/science/article/pii/S1043661815000833>
::: Website <http://www.parhamacademy.com/news.php>
------------------------------
Message: 4
Date: Sat, 26 Sep 2015 14:44:36 -0300
From: Juliano Braz Carregal <julianocarregal at hotmail.com<mailto:julianocarregal at hotmail.com>>
To: gromacs.org_gmx-users at maillist.sys.kth.se<mailto:gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Restart simulation after crash
Message-ID: <SNT406-EAS23559A58A012A4725F9826B8410 at phx.gbl<mailto:SNT406-EAS23559A58A012A4725F9826B8410 at phx.gbl>>
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Message: 5
Date: Sat, 26 Sep 2015 13:47:27 -0400
From: Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>>
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Re: [gmx-users] Restart simulation after crash
Message-ID: <5606DA2F.20101 at vt.edu<mailto:5606DA2F.20101 at vt.edu>>
Content-Type: text/plain; charset=windows-1252; format=flowed
Please don't reply to the entire digest, especially when you're not replying to
anything related.
On 9/26/15 1:44 PM, Juliano Braz Carregal wrote:
> Hi everyone,its possible to restart a MD simulation just after the power
> crashing instead restart from the beginning?thanks
>
Of course.
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
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