[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 35

Wed Mar 9 02:27:02 CET 2016

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-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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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.szilard at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Details of 5.0 benchmark report?
Message-ID:
    <CANnYEw48HvMDbWtG8WYopyHU1Pdie_r0LfVH5m_faqkHJC=MxQ at 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.huffman at 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
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------------------------------

Message: 2
Date: Tue, 8 Mar 2016 13:20:49 -0600
From: Parvez Mh <parvezmh89 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] apply force on single molecule
Message-ID:
    <CAJU_nuU787mVTAxSRq8wiTdk2a9+3=W1Zpt0zxtLESF5n1AoqA at 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." <smithmd at ornl.gov>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] apply force on single molecule
Message-ID: <1457465394988.73318 at 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-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Parvez Mh <parvezmh89 at gmail.com>
Sent: Tuesday, March 08, 2016 2:20 PM
To: gromacs.org_gmx-users at 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
--
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------------------------------

Message: 4
Date: Wed, 9 Mar 2016 00:21:50 +0000
From: Ming Tang <m21.tang at qut.edu.au>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
    <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] fix COM
Message-ID:
    <BY2PR01MB169D379E015F07C5E88760FB6B30 at 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 <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Neutralizing
Message-ID: <56DF74B0.9070701 at 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) <pjabbarzadeh at 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.r0325 at 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
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>
>
>
>

-- 
==================================================

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 | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

------------------------------

Message: 6
Date: Tue, 8 Mar 2016 19:57:27 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] distance restraints in mdp
Message-ID: <56DF74F7.7070005 at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

------------------------------

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End of gromacs.org_gmx-users Digest, Vol 143, Issue 35
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