dear Justin Lemkuli already run that without restraints, it has no problems.
even i used the gro file from the simple 5ns MD but still have these same
errors and warnings. when i set Lincs constraints to all-bonds , simulation
finishes fine but by using alchemical_analysis.py for free energies it gives
errors and warnings. (Warning: states 29 and 37 have the same energies on the
dataset.) i used 42 lambdas and about 32 states are having same energies. and
when i set constraints to h-bonds then LINCS warnings. i tried to use different
options for pressure coupling also because i read somewhere it also affects
simulation. i am quite confused where the problem is. is it possible to send
you topology file and you have a look?Thanks in advance Sana Saeed
Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS
bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.
On Wednesday, March 9, 2016 9:58 AM,
"gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
<gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
Send gromacs.org_gmx-users mailing list submissions to
gromacs.org_gmx-users@maillist.sys.kth.se
To subscribe or unsubscribe via the World Wide Web, visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
gromacs.org_gmx-users-requ...@maillist.sys.kth.se
You can reach the person managing the list at
gromacs.org_gmx-users-ow...@maillist.sys.kth.se
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."
Today's Topics:
1. Re: Details of 5.0 benchmark report? (Szil?rd P?ll)
2. apply force on single molecule (Parvez Mh)
3. Re: apply force on single molecule (Smith, Micholas D.)
4. Re: fix COM (Ming Tang)
5. Re: Neutralizing (Justin Lemkul)
6. Re: distance restraints in mdp (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Tue, 8 Mar 2016 18:08:20 +0100
From: Szil?rd P?ll <pall.szil...@gmail.com>
To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Details of 5.0 benchmark report?
Message-ID:
<CANnYEw48HvMDbWtG8WYopyHU1Pdie_r0LfVH5m_faqkHJC=m...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
What details are you interested in? IIRC the inputs are clearly specified
(although perhaps not provided there).
--
Szil?rd
On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman <adam.huff...@gmail.com> wrote:
> Hello
>
> Are details of the running of the benchmarks reported for version 5.0
> available anywhere?
>
> I'm referring to the report published at:
>
> http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf
>
> I would like to be able to run these myself, on three different systems.
>
>
> Cheers,
> Adam
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
------------------------------
Message: 2
Date: Tue, 8 Mar 2016 13:20:49 -0600
From: Parvez Mh <parvezm...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] apply force on single molecule
Message-ID:
<CAJU_nuU787mVTAxSRq8wiTdk2a9+3=w1zpt0zxtlesf5n1a...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear all,
I want look at change in potential energy profile, when i apply force on a
molecule on one end where other end fixed in a position. Is it possible do
it in gromacs. If yes, how may i proceed?
--Masrul
------------------------------
Message: 3
Date: Tue, 8 Mar 2016 19:29:54 +0000
From: "Smith, Micholas D." <smit...@ornl.gov>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] apply force on single molecule
Message-ID: <1457465394988.73...@ornl.gov>
Content-Type: text/plain; charset="iso-8859-1"
Yes. Take a look at the manual for information on using the Pulling code.
===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Parvez Mh
<parvezm...@gmail.com>
Sent: Tuesday, March 08, 2016 2:20 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] apply force on single molecule
Dear all,
I want look at change in potential energy profile, when i apply force on a
molecule on one end where other end fixed in a position. Is it possible do
it in gromacs. If yes, how may i proceed?
--Masrul
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
------------------------------
Message: 4
Date: Wed, 9 Mar 2016 00:21:50 +0000
From: Ming Tang <m21.t...@qut.edu.au>
To: "gromacs.org_gmx-users@maillist.sys.kth.se"
<gromacs.org_gmx-users@maillist.sys.kth.se>
Subject: Re: [gmx-users] fix COM
Message-ID:
<by2pr01mb169d379e015f07c5e88760fb6...@by2pr01mb169.prod.exchangelabs.com>
Content-Type: text/plain; charset="us-ascii"
Thank you Justin,
The flat-bottom position restraint fixed my problem indeed.
------------------------------
Message: 5
Date: Tue, 8 Mar 2016 19:56:16 -0500
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Neutralizing
Message-ID: <56df74b0.9070...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 3/8/16 3:59 AM, mohammad r wrote:
> Thank you Parham
> You mean that it is not necessary to do QM/MM simulation?
>
The trivial task of adding ions to neutralize the net charge on the system
certainly does not require anything like QM/MM.
-Justin
> On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of
>Biomedical Science) <pjabbarza...@gmail.com> wrote:
>
>
> Dear Sir
>
> Use this command:
>
> gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral
>
> In this case, you don't need ?the number of ions?.
> Kind Regards
>
> Parham J. K.
> ??????======?======?=============
> ?PhD candidate - Lecturer in drug discovery
> Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia
> ?======?===================Publication ::: Featured Publication ::: Website
> ::: FaceBook
> On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0...@yahoo.com> wrote:
>
> Hi everybody, I?ve generated a water-peptide system, now I want to neutralize
> it. Is adding adequate number of ions sufficient for neutralizing process or
> I should do QM/MM simulation for the this process? Thank you, Mohammad.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
>
>
>
>
>
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 6
Date: Tue, 8 Mar 2016 19:57:27 -0500
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] distance restraints in mdp
Message-ID: <56df74f7.7070...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 3/7/16 10:35 PM, Sana Saeed wrote:
> i am performing protein ligand binding free energy calculation MD. i have
> applied distance restraint to 1 pair of atoms. now when i am running md it
> gives me LINCS warnings. first i thought it is because of wrong geometry so i
> changed complex, now i am doing it for Lysozyme+JZ4. but still same warning.
> i am confused about the distance restraints to be introduced in mdp file.
> disre = simple/ensemble? i read in manual, but still confused. i tried both
> with "simple it gives me LINCS warning and with ensemble it says that this
> version of gromacs doesnt support it. i am using 5.1 gromacs.
Then simplify further and make sure the system runs without restraints or
anything else. Just normal MD. Start simple to avoid chasing the wrong
problem.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
End of gromacs.org_gmx-users Digest, Vol 143, Issue 35
******************************************************
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
