[gmx-users] VMD visualization of clusters
Hi GMX users, After visualization of one of my clusters generated by g-cluster command in gromacs , i couldn't change the representation type in VMD from lines to new cartoon or secondary structure so i am wondering if this is related to the structure of cluster ? ... why i can visualize the cluster only in lines ? Thank you! -- *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.
[gmx-users] how to keep the ligand inside water box
Hi GMX users, After running nvt equilibration, my ligand get out the box and before proceeding to npt equilibration i want to know how to get (and keep if is it possible) the ligand in water box* center* ? Thank you ! -- *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.
[gmx-users] Subject: Re: Group WAT referenced in the .mdp file was not found in the index file
Hi Justin, Thanks for your response, I am using a topology file constructed from amber tools ... -- *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.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 40
o we can't say. > > Let solvate and genion do the work for you. Use the -p flag to have > those programs update your topology for you, especially if you are not > familiar with their contents or how to edit them. See e.g. > http://www.mdtutorials.com/gmx/lysozyme/index.html > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > > > -- > > Message: 3 > Date: Tue, 13 Nov 2018 00:01:24 + > From: Ali Khodayari > To: "gmx-us...@gromacs.org" > Subject: Re: [gmx-users] pdb2gmx fatal error > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Dear Justin, > > Thank you for your full explanation. That made it all clear now. > > Kind regards, > Ali > > > On 13 Nov 2018, at 00:57, Justin Lemkul wrote: > > > > > > > > On 11/8/18 1:37 PM, Ali Khodayari wrote: > >> Dear Justin, > >> > >> Thank you for your response. Yet, I have not been able to solve the > problem. > >> > >> The structure looks fine but gromacs is complaining about a dangling > atom at > >> one of the terminal ends, if I choose no terminal to be added. While, > > > > You can't "see" a dangling bond by visualizing the structure. That term > refers exclusively to an incomplete terminus in terms of the *topology* > that is being generated for the system. Maybe atoms are missing or an > inappropriate terminal patch is being applied; either would generate that > error. But again I emphasize the fact that a chain of glucose has first and > last residues that are structurally and topologically different from > internal, linked monomers. It's basic chemistry. > > > > > > > >> ATOM 27 O3 GLC02 3.909 5.661 5.002 1.00 0.04 > >> O > >> ATOM 28 HO4 GLC02 4.850 3.729 10.263 1.00 0.00 > >> H > >> ATOM 29 O1 GLC01 3.396 2.685 4.467 1.00 0.04 > >> O > > > > Here's your problem - your residue numbers alternate back and forth > between 1 and 2. pdb2gmx ignores these and uses its own numbering, > incrementing the internal counter whenever the residue number changes. So > to pdb2gmx, your input file is full of incomplete residues. > > > >> ATOM 30 O5 GLC02 4.225 2.770 8.173 1.00 0.04 > >> O > >> ATOM 31 O6 GLC02 3.558 0.309 5.328 1.00 0.04 > >> O > >> ATOM 32 H1 GLC02 2.572 4.115 8.609 1.00 0.00 > >> H > >> ATOM 33 H2 GLC02 5.244 5.151 7.307 1.00 0.00 > >> H > >> ATOM 34 H3 GLC02 2.361 4.651 6.153 1.00 0.00 > >> H > >> ATOM 35 H4 GLC02 5.141 3.258 5.636 1.00 0.00 > >> H > >> ATOM 36 H5 GLC02 2.480 2.262 6.979 1.00 0.00 > >> H > >> ATOM 37 H61 GLC02 3.879 0.196 7.468 1.00 0.00 > >> H > >> ATOM 38 H62 GLC02 5.286 0.920 6.494 1.00 0.00 > >> H > >> ATOM 39 HO2 GLC02 2.496 6.480 7.836 1.00 0.00 > >> H > >> ATOM 40 HO3 GLC02 5.015 5.674 4.919 1.00 0.00 > >> H > >> ATOM 41 HO6 GLC02 2.453 0.270 5.418 1.00 0.00 > >> H > >> ATOM 42 O3 GLC01 3.852 1.653 -0.348 1.00 0.00 > >> O > > > > As above, now you're again going back and forth between 1 and 2, so > pdb2gmx sees a new residue, which is not correct. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Virginia Tech Department of Biochemistry > > > > 303 Engel Hall > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > == > > > > -- > > 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 request
[gmx-users] Group WAT referenced in the .mdp file was not found in the index file
Hi GMX users, i double checked in my topology and gro files that i am using the same moleculetype ( LIG and WAT) but when i run grompp for T equilibration i get an error message """" Group WAT referenced in the .mdp file was not found in the index file """" PS: i am not using an index file and i modified tc-grps, in nvt.mdp file , to : tc-grps = LIG WAT . Thank you ! Best Regards -- *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.
[gmx-users] Error in running energy minimization
Hi GMX users, I am running energy minimization for my ligand in water box , I have manually constructed a topology file for my ligand (with antechamber tools) and i introduced all the necessary atomtypes, even for water molecules ( i created *itp file*, named water.itp, where i include the defintions of water atom types and all their necessary parameters like in tip3p.itp water model in amber ) but unfortunately when i used 'grompp' command to run energy minimization it* didn't recognize OW atom type , *when i replaced atom-Type, inside itp file, by *oh *which is not correct to describe water oxygen atoms but it worked for energy minimization and *the job run normally* which is weird since in amber atom type OW (water) is different from OH (hydroxyl) atomtype. please find enclosed my water.itp file with modified water atomtype (oh, ho, ho), where i used amber water parameters for tip3p model. and my questions are *:* why 'grompp' didin't recognize OW atomtype even if i already included all the necessary definitions of atomtypes ? and Is it OK to use hydroxyl atomtype to describe water atoms ? Can you help me please, Thank you ! -- *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.
[gmx-users] Topology include file "tip3p.itp" not found
Dear Gromacs Users, I want to run MD simulation of ligand in water box , for that i have manually constructed a topology file of my ligand with antechamber tools then i used GROMACS instructions to build a box of water molecules (ligand_solv.gro), when i tried to minimize my structure (with grompp) i get this error """ *atomtype OW is not found* """" then i create manually tip3p.itp file (which contains tip3p parameters) to identify the water atom types and i added in my topology file the following commands: ; Include water topology #include "tip3p.itp" But i always get this error Topology include file "tip3p.itp" not found Can you help me please, Thank you ! -- *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.
[gmx-users] atomtype OW is not found
Hi Gromacs users, I used antechamber tools to genrate a topology and coordinates files for my ligand, then i used acpype to convert them to gromacs files (.top and .gro), then *i added manually water FF in topology file* since i want to run MD simulation of ligand in water I double checked the notation of water molecule (OW and HW) in gro file but i always get this error """ *atomtype OW is not found* """" here I copy paste a part of my topology file where i include water FF ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif Can anyone help me please, Thank you -- *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.
[gmx-users] Newton Raphson Method
Hi, Is it possible to use Newton Raphson Method for energy minimization in gromacs ? and what keyword to use as integrator inside the minim.mdp file ? Thank you -- *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.
[gmx-users] missing atoms in residues
Hi everyone, I have one question: Is it possible to add missing atoms in residues using gromacs ? ( PS. i already tried pdb2gmx but it didn't work out) missing atoms are : GLU A 117CB CG CD OE1 OE2 PRO A 158CB CG CD Thank you! -- *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.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 39
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>: > 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. 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 + (UTC) > From: Anjana Jayasinghe > To: Discussion List for GROMACS Users > 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 > 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 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Problem in generation of tpr file > Message-ID: > 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 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problem in generation of tpr file > Message-ID: > 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 informat
[gmx-users] Problem in generation of tpr file
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 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.
[gmx-users] gromacs error
Hi, How can i rectify the following GROMACS error? Fatal error: atom HN2 in residue LYS2 was not found in rtp enetry NYLS with 24 atoms while sorting atoms. Thank you for your help -- *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.
[gmx-users] How to extend the protein simulation in Gromacs from 1 ns to 150 ns?
Hi, i am a beginner with Gromacs and i have run the simulation using Gromacs forcefield for 1000 ps* (1ns)* . Now I want to extend it to *150 ns*. How should I proceed? should i change the md.mdp file ?? actually i am using the defaul mdp file in gromacs tutorial : integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 f so what should i change exactly?? can anyone help me please, Thank you -- *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.
[gmx-users] problem on Gromacs 4.5.7 installation
Dear gmx-users, I am trying to install Gromacs 4.5.7 and i choose to run it with cmake 3.9.0 and fftw 3.3.6 i succeeded to install cmake files but i have a problem with fftw installtion: its a 'make install' problem: make[3]: *** [install-includeHEADERS] Erreur 1 make[3]: quittant le répertoire « /home/rahma/Bureau/simulation_dynamique/fftw-3.3.6-pl2/api » make[2]: *** [install-am] Erreur 2 make[2]: quittant le répertoire « /home/rahma/Bureau/simulation_dynamique/fftw-3.3.6-pl2/api » make[1]: *** [install] Erreur 2 make[1]: quittant le répertoire « /home/rahma/Bureau/simulation_dynamique/fftw-3.3.6-pl2/api » make: *** [install-recursive] Erreur 1 I am wondering if there is a special version of fftw to run it with gromacs 4.5.7 ? Thank you -- *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.
[gmx-users] problem on Gromacs 4.5.7 installation
Hi, I'am a phd student, i need to work with gromacs version 4.57 but i have an installation problem, i apply all the instructions of installation but i have always the 'make install' problem. I really need to work with gromacs (4.5.7) for my work Best regards -- *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.
