[gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 39

Mon Jun 11 12:51:34 CEST 2018

sorry, i am new Gromacs user, where i can find the warning text ?

2018-06-11 11:00 GMT+01:00 <
gromacs.org_gmx-users-request at maillist.sys.kth.se>:

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> Today's Topics:
>
>    1. Hexagonal Phase modelling (Anjana Jayasinghe)
>    2. Re: Hexagonal Phase modelling (David van der Spoel)
>    3. Problem in generation of tpr file (Rahma Dahmani)
>    4. Re: Problem in generation of tpr file (Alex)
>    5. Doubts in combination rules 2 and 3 (Apramita Chand)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 10 Jun 2018 13:51:58 +0000 (UTC)
> From: Anjana Jayasinghe <anjusilva90 at yahoo.com>
> To: Discussion List for GROMACS Users <gmx-users at gromacs.org>
> Subject: [gmx-users] Hexagonal Phase modelling
> Message-ID: <1474481440.2702954.1528638718718 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
> I want to model a hexagonal phase and do? MD simulations using gromacs.
> Could you please guide me to model a hexagoanl phase for my CiEj molecules?
> Thank you.
>
> ------------------------------
>
> Message: 2
> Date: Sun, 10 Jun 2018 17:21:39 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Hexagonal Phase modelling
> Message-ID: <158d03e2-8fa4-b8ff-1d42-cf23b26bc9ad at xray.bmc.uu.se>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Den 2018-06-10 kl. 15:51, skrev Anjana Jayasinghe:
> > Dear Gromacs users,
> > I want to model a hexagonal phase and do? MD simulations using gromacs.
> Could you please guide me to model a hexagoanl phase for my CiEj molecules?
> > Thank you.
> >
> You can simulate any kind of periodicity that can be descirbed by a
> triclinic box, that probably includes your data. Just give gromacs a
> correct pdb file with CRYST1 entry.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 11 Jun 2018 09:48:51 +0100
> From: Rahma Dahmani <rahma.dahmani at fst.utm.tn>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Problem in generation of tpr file
> Message-ID:
>         <CADeDvBEkNZUbkMHn+X_HKT8QqgtHn8kQVw_04c=99LW8SfY17
> A at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi gmx users,
>
> I am performing Molecular Dynamic simulations of protein-ligand complex by
> following steps shown in "GROMACS Tutorials.  While moving on to
> production MD,
> i coudn't generate the tpr file, in fact i only activated velocity
> generation parameter in my md.mdp file, and it shows this error:
>
> Program grompp, VERSION 4.5.7
> Source code file:
> /home/rahma/Bureau/CODE/GROMACS/gromacs-4.5.7/src/kernel/grompp.c, line:
> 1611
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> when velocity generation was off i didn't get this error.....
>
> can anyone help me please
>
> Thank you!
>
>
>
> --
>
>
>
>
>
>
> *Rahma Dahmani Doctorante en CHIMIE Unit? de Recherche: Physico-Chimie des
> Mat?riaux ? l'?tat condens?, Laboratoire de Chimie Th?orique et
> Spectroscopie Mol?culaireUniversit? de Tunis El Manar, Facult? des Sciences
> de Tunis Campus Universitaire Farhat Hached - BP n ? 94 - Rommana 1068,
> Tunisie T?l: (+216) 28151042*
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 11 Jun 2018 02:53:50 -0600
> From: Alex <nedomacho at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem in generation of tpr file
> Message-ID: <a3fba232-0e64-8bc0-9d75-e4ce7c249f45 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Grompp tells you exactly what to do:
>
> "Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors"
>
> Read the text of the warning and if you decide it's not serious, add
> something like -maxwarn 2 at the end of your grompp line.
>
> Alex
>
>
> On 6/11/2018 2:48 AM, Rahma Dahmani wrote:
> > Hi gmx users,
> >
> > I am performing Molecular Dynamic simulations of protein-ligand complex
> by
> > following steps shown in "GROMACS Tutorials.  While moving on to
> production MD,
> > i coudn't generate the tpr file, in fact i only activated velocity
> > generation parameter in my md.mdp file, and it shows this error:
> >
> > Program grompp, VERSION 4.5.7
> > Source code file:
> > /home/rahma/Bureau/CODE/GROMACS/gromacs-4.5.7/src/kernel/grompp.c, line:
> > 1611
> > Fatal error:
> > Too many warnings (1), grompp terminated.
> > If you are sure all warnings are harmless, use the -maxwarn option.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > when velocity generation was off i didn't get this error.....
> >
> > can anyone help me please
> >
> > Thank you!
> >
> >
> >
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 11 Jun 2018 14:50:47 +0530
> From: Apramita Chand <apramita.chand at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Doubts in combination rules 2 and 3
> Message-ID:
>         <CA+gTzoZAmuZ+zmNeYZXzbbWiUG3FEyZ3jnQ002TBmU
> WthbO_yQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Please clarify these following doubts regarding combination rules in gromos
> force field:
>
> 1. The ffnonbonded.itp contains c6, c12 terms. If I choose combination rule
> 1 , it takes V and W as C6 and C12 as given. If combination 2 or 3 are
> chosen , then are the values converted to sigma and epsilon (Since for
> V=sigma and W=epsilon) and then used?
> 2. If I have sigma and epsilon values for my molecule of interest, how do I
> add them to ffnonbonded.itp? Can I directly include sigma value under C6
> and epsilon value under C12 column?
> And then specify combination rule as 2 or 3?
>
> If so, how should I modify the non-bonded params section?
> Should I compute the interactions between atoms(according to the
> combination rule) and include them prior to simulation??
>
> Thanking you,
> Yours sincerely,
> Apramita
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 170, Issue 39
> ******************************************************
>

-- 

*Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
Tunisie Tél: (+216) 28151042*