<p dir="ltr">Can someone tell me a good program/sever besides prodg ,to generate topology for organic and inorganic ligands.thanks</p>
<div class="quote">Em 26/09/2015 2:48 PM, gromacs.org_gmx-users-request@maillist.sys.kth.se escreveu:<br type='attribution'><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
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Today's Topics:<br />
<br />
1. bonded forces in output (Stanislav ?imko)<br />
2. Re: bonded forces in output (Justin Lemkul)<br />
3. Installation problem<br />
(Parham Jabbarzadeh (Department of Biomedical Science))<br />
4. Restart simulation after crash (Juliano Braz Carregal)<br />
5. Re: Restart simulation after crash (Justin Lemkul)<br />
<br />
<br />
----------------------------------------------------------------------<br />
<br />
Message: 1<br />
Date: Sat, 26 Sep 2015 11:31:24 +0200<br />
From: Stanislav ?imko <stanislav.simko@gmail.com><br />
To: gromacs.org_gmx-users@maillist.sys.kth.se<br />
Subject: [gmx-users] bonded forces in output<br />
Message-ID: <1443259884.25179.9.camel@gmail.com><br />
Content-Type: text/plain; charset="UTF-8"<br />
<br />
Dear gromacs users,<br />
I'm writing my code to calculate pressure from trajectory files - from<br />
problthat em atomic positions and forces - according to virial theorem.<br />
Currently, I'm able to calculate the same pressure when I've got only<br />
non-bonded forces of a small system (10 atoms with charges and LJ<br />
parameters) centered in a big (100nm cubic) box. Hopefully, my code<br />
should work also for smaller box where atoms can see periodic images.<br />
The problem that I'm facing right now is that I do not know how to<br />
obtain bonded forces from the trajectory files. E.g., for single spc<br />
water molecule gromacs gives zero forces on all atoms, even though I<br />
assigned them different velocities.<br />
to obtain forces I run:<br />
gmx traj -f *.trr -s *.tpr -of forces -fp<br />
Also, gromacs gives me non-zero virial (diagonal elements XX, YY, ZZ),<br />
which means that there are some forces<br />
gmx energy -f *.edr -s *.tpr ...<br />
So I would like to ask, if there is some way how to get bonded forces<br />
out of the trajectory... (or rerun with some runtime parameters to<br />
force gromacs to print bonded forces)<br />
Sincerely,<br />
stanislav.<br />
<br />
<br />
------------------------------<br />
<br />
Message: 2<br />
Date: Sat, 26 Sep 2015 12:02:48 -0400<br />
From: Justin Lemkul <jalemkul@vt.edu><br />
To: gmx-users@gromacs.org<br />
Subject: Re: [gmx-users] bonded forces in output<br />
Message-ID: <5606C1A8.4090106@vt.edu><br />
Content-Type: text/plain; charset=windows-1252; format=flowed<br />
<br />
<br />
<br />
On 9/26/15 5:31 AM, Stanislav ?imko wrote:<br />
> Dear gromacs users,<br />
> I'm writing my code to calculate pressure from trajectory files - from<br />
> problthat em atomic positions and forces - according to virial theorem.<br />
> Currently, I'm able to calculate the same pressure when I've got only<br />
> non-bonded forces of a small system (10 atoms with charges and LJ<br />
> parameters) centered in a big (100nm cubic) box. Hopefully, my code<br />
> should work also for smaller box where atoms can see periodic images.<br />
> The problem that I'm facing right now is that I do not know how to<br />
> obtain bonded forces from the trajectory files. E.g., for single spc<br />
> water molecule gromacs gives zero forces on all atoms, even though I<br />
> assigned them different velocities.<br />
> to obtain forces I run:<br />
> gmx traj -f *.trr -s *.tpr -of forces -fp<br />
> Also, gromacs gives me non-zero virial (diagonal elements XX, YY, ZZ),<br />
> which means that there are some forces<br />
> gmx energy -f *.edr -s *.tpr ...<br />
> So I would like to ask, if there is some way how to get bonded forces<br />
> out of the trajectory... (or rerun with some runtime parameters to<br />
> force gromacs to print bonded forces)<br />
<br />
By default, water is treated as rigid via SETTLE, so there are no bonded forces. <br />
You can turn this off with "define = -DFLEXIBLE" in the .mdp file for the <br />
purpose of do a re-calculation of energies and forces.<br />
<br />
-Justin<br />
<br />
-- <br />
==================================================<br />
<br />
Justin A. Lemkul, Ph.D.<br />
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
<br />
Department of Pharmaceutical Sciences<br />
School of Pharmacy<br />
Health Sciences Facility II, Room 629<br />
University of Maryland, Baltimore<br />
20 Penn St.<br />
Baltimore, MD 21201<br />
<br />
jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br />
<a href="http://mackerell.umaryland.edu/~jalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br />
<br />
==================================================<br />
<br />
<br />
------------------------------<br />
<br />
Message: 3<br />
Date: Sat, 26 Sep 2015 09:08:08 -0700<br />
From: "Parham Jabbarzadeh (Department of Biomedical Science)"<br />
<pjabbarzadeh@gmail.com><br />
To: gromacs.org_gmx-users@maillist.sys.kth.se<br />
Subject: [gmx-users] Installation problem<br />
Message-ID:<br />
<CAGq_gb8tUi4aYyEGRL3S8smKkcWjkcQ4C2-wBtDA78zD1DsNgg@mail.gmail.com><br />
Content-Type: text/plain; charset=UTF-8<br />
<br />
Dear sir<br />
<br />
When I am installing in the build directory, I faced the folliwng error.<br />
Can you help me? My Ubuntu version is 15.04.<br />
<br />
Issue another request to this URL:<br />
'<a href="https://kth.box.com/shared/static/53xl0qouhsvrbrbgtl4p.gz">https://kth.box.com/shared/static/53xl0qouhsvrbrbgtl4p.gz</a>'<br />
<br />
Protocol "https" not supported or disabled in libcurl<br />
<br />
Closing connection -1<br />
<br />
<br />
<br />
-- Configuring incomplete, errors occurred!<br />
<br />
<br />
Thanks<br />
<br />
<br />
<br />
<br />
<br />
*?Parham Jabbarzadeh Kaboli*=========================<br />
??<br />
========<br />
?========?<br />
<br />
Cancer Pharmacologist<br />
Faculty of Medicine and Health Sciences<br />
University Putra Malaysia<br />
Malaysia<br />
<br />
=================================<br />
?========?<br />
<br />
Publication <<a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=Parham+Jabbarzadeh+Kaboli">http://www.ncbi.nlm.nih.gov/pubmed/?term=Parham+Jabbarzadeh+Kaboli</a>>:::<br />
Featured Publication<br />
<<a href="http://www.sciencedirect.com/science/article/pii/S1043661815000833">http://www.sciencedirect.com/science/article/pii/S1043661815000833</a>><br />
::: Website <<a href="http://www.parhamacademy.com/news.php">http://www.parhamacademy.com/news.php</a>><br />
<br />
<br />
------------------------------<br />
<br />
Message: 4<br />
Date: Sat, 26 Sep 2015 14:44:36 -0300<br />
From: Juliano Braz Carregal <julianocarregal@hotmail.com><br />
To: gromacs.org_gmx-users@maillist.sys.kth.se<br />
Subject: [gmx-users] Restart simulation after crash<br />
Message-ID: <SNT406-EAS23559A58A012A4725F9826B8410@phx.gbl><br />
Content-Type: text/plain; charset="us-ascii"<br />
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An HTML attachment was scrubbed...<br />
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<br />
------------------------------<br />
<br />
Message: 5<br />
Date: Sat, 26 Sep 2015 13:47:27 -0400<br />
From: Justin Lemkul <jalemkul@vt.edu><br />
To: gmx-users@gromacs.org<br />
Subject: Re: [gmx-users] Restart simulation after crash<br />
Message-ID: <5606DA2F.20101@vt.edu><br />
Content-Type: text/plain; charset=windows-1252; format=flowed<br />
<br />
<br />
Please don't reply to the entire digest, especially when you're not replying to <br />
anything related.<br />
<br />
On 9/26/15 1:44 PM, Juliano Braz Carregal wrote:<br />
> Hi everyone,its possible to restart a MD simulation just after the power<br />
> crashing instead restart from the beginning?thanks<br />
><br />
<br />
Of course.<br />
<br />
<a href="http://www.gromacs.org/Documentation/How-tos/Doing_Restarts">http://www.gromacs.org/Documentation/How-tos/Doing_Restarts</a><br />
<br />
-Justin<br />
<br />
-- <br />
==================================================<br />
<br />
Justin A. Lemkul, Ph.D.<br />
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br />
<br />
Department of Pharmaceutical Sciences<br />
School of Pharmacy<br />
Health Sciences Facility II, Room 629<br />
University of Maryland, Baltimore<br />
20 Penn St.<br />
Baltimore, MD 21201<br />
<br />
jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br />
<a href="http://mackerell.umaryland.edu/~jalemkul">http://mackerell.umaryland.edu/~jalemkul</a><br />
<br />
==================================================<br />
<br />
<br />
------------------------------<br />
<br />
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</blockquote></div>