Re: [gmx-users] Problem in generation of tpr file
On 6/11/18 2:42 PM, Alex wrote: To be clear, I did suggest ignoring it _only_ if the warning is: a) understood, b) of known origin, and c) harmless. I am not sure what's your one case is when ignoring warnings is appropriate, but I routinely use '-maxwarn 10,' because I have a bunch of bonded parameters that override default stuff in ffbonded for DNA (I think this customization came from Tsjerk Wassenaar when we collaborated). The warnings appear even when no DNA is present in the system, but in either case I know exactly what I am doing. In no way should new users interpret my suggestion as "it is okay to ignore grompp warnings." It is NOT okay to ignore them. Right, and I only pointed it out because the OP seemed confused about what's going on, so I felt it important to reinforce the fact that new users should never use this option. The one case I remember requiring -maxwarn was with MARTINI, which set up dummy atom names in its coordinate files, only to be corrected later in grompp so that the topology atom names were used. This appears to no longer be the case, so I can now think of precisely ZERO times that -maxwarn should be employed in common usage. Your broken, conflicting force fields would be an intermediate-level exception :) The problem I've seen is when people see existing scripts/workflows with -maxwarn 10 (living dangerously!) then it gets propagated without thought. Hopefully all of your scripts and protocols come with the comment of "DON'T DO THIS GENERALLY" :) -Justin Alex On 6/11/2018 6:04 AM, Justin Lemkul wrote: Please don't respond to the entire digest, and if you're actively asking questions, I suggest changing your list subscription to receive individual emails. On 6/11/18 6:51 AM, Rahma Dahmani wrote: sorry, i am new Gromacs user, where i can find the warning text ? grompp prints very clear and obvious WARNINGs to the terminal. Read what it says. I disagree with Alex's suggestion that using -maxwarn might be appropriate. There's basically only one case I can think of when this is ever reasonable, yet I see people get in trouble all the time when they start making a habit of using -maxwarn. grompp is trying to tell you that what you are doing is physically unreasonable. Don't ignore it. -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 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] Problem in generation of tpr file
To be clear, I did suggest ignoring it _only_ if the warning is: a) understood, b) of known origin, and c) harmless. I am not sure what's your one case is when ignoring warnings is appropriate, but I routinely use '-maxwarn 10,' because I have a bunch of bonded parameters that override default stuff in ffbonded for DNA (I think this customization came from Tsjerk Wassenaar when we collaborated). The warnings appear even when no DNA is present in the system, but in either case I know exactly what I am doing. In no way should new users interpret my suggestion as "it is okay to ignore grompp warnings." It is NOT okay to ignore them. Alex On 6/11/2018 6:04 AM, Justin Lemkul wrote: Please don't respond to the entire digest, and if you're actively asking questions, I suggest changing your list subscription to receive individual emails. On 6/11/18 6:51 AM, Rahma Dahmani wrote: sorry, i am new Gromacs user, where i can find the warning text ? grompp prints very clear and obvious WARNINGs to the terminal. Read what it says. I disagree with Alex's suggestion that using -maxwarn might be appropriate. There's basically only one case I can think of when this is ever reasonable, yet I see people get in trouble all the time when they start making a habit of using -maxwarn. grompp is trying to tell you that what you are doing is physically unreasonable. Don't ignore it. -Justin -- 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] Problem in generation of tpr file
Please don't respond to the entire digest, and if you're actively asking questions, I suggest changing your list subscription to receive individual emails. On 6/11/18 6:51 AM, Rahma Dahmani wrote: sorry, i am new Gromacs user, where i can find the warning text ? grompp prints very clear and obvious WARNINGs to the terminal. Read what it says. I disagree with Alex's suggestion that using -maxwarn might be appropriate. There's basically only one case I can think of when this is ever reasonable, yet I see people get in trouble all the time when they start making a habit of using -maxwarn. grompp is trying to tell you that what you are doing is physically unreasonable. Don't ignore it. -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 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] Problem in generation of tpr file
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! -- 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 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.
