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-requ...@maillist.sys.kth.se>:
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Doubts in combination rules 2 and 3 (Apramita Chand) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 10 Jun 2018 13:51:58 +0000 (UTC) > From: Anjana Jayasinghe <anjusilv...@yahoo.com> > To: Discussion List for GROMACS Users <gmx-us...@gromacs.org> > Subject: [gmx-users] Hexagonal Phase modelling > Message-ID: <1474481440.2702954.1528638718...@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 <sp...@xray.bmc.uu.se> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Hexagonal Phase modelling > Message-ID: <158d03e2-8fa4-b8ff-1d42-cf23b26bc...@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.dahm...@fst.utm.tn> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Problem in generation of tpr file > Message-ID: > <CADeDvBEkNZUbkMHn+X_HKT8QqgtHn8kQVw_04c=99LW8SfY17 > a...@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 <nedoma...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problem in generation of tpr file > Message-ID: <a3fba232-0e64-8bc0-9d75-e4ce7c249...@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.ch...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] Doubts in combination rules 2 and 3 > Message-ID: > <CA+gTzoZAmuZ+zmNeYZXzbbWiUG3FEyZ3jnQ002TBmU > wthbo...@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 > > > ------------------------------ > > -- > 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 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* -- 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.