From fjanatifard at gmail.com Wed Aug 5 19:29:20 2020 From: fjanatifard at gmail.com (F Janati) Date: Wed, 05 Aug 2020 17:29:20 -0000 Subject: [gmx-developers] (no subject) Message-ID: My structure consist of single strand DNA (26 mer). I cut 2 mer from n-teminous and 2 mer from c-terminous of DNA. After pdb2gmx command and choose Amber force field ,I got some following error like this: "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms while sorting atoms." I would be very grateful if you guide me. Best wishes From johnwhittake at zedat.fu-berlin.de Wed Aug 5 19:48:47 2020 From: johnwhittake at zedat.fu-berlin.de (John Whittaker) Date: Wed, 05 Aug 2020 17:48:47 -0000 Subject: [gmx-developers] (no subject) In-Reply-To: References: Message-ID: <54198.80.137.46.59.1596649725.webmail@webmail.zedat.fu-berlin.de> Hi, > My structure consist of single strand DNA (26 mer). > I cut 2 mer from n-teminous and 2 mer from c-terminous of DNA. > After pdb2gmx command and choose Amber force field ,I got some > following error like this: > "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms > while sorting atoms." This mailing list is for GROMACS developers. Please direct all GROMACS usage questions to the GROMACS forum at: https://gromacs.bioexcel.eu/ Also, give more information about what you did and include a subject. "After pdb2gmx command..." is too vague, give the command you used. This is also useful to read before you ask the forum: http://manual.gromacs.org/documentation/2018.1/user-guide/run-time-errors.html Under section "Atom X in residue YYY not found in rtp entry" Best, ---------------------------------------- John Whittaker Ph.D. Candidate Department of Mathematics and Computer Science Freie Universit?t Berlin +49 0160 936 04221 From srivastava.2 at iitj.ac.in Fri Aug 7 10:21:15 2020 From: srivastava.2 at iitj.ac.in (Abhinav Srivastava (P14CHM002)) Date: Fri, 07 Aug 2020 08:21:15 -0000 Subject: [gmx-developers] Surface tension of bulk water Message-ID: Dear Gromacs Users, I am trying to calculate the surface tension of bulk water. I am using TIP4P/2005 water model consisting of 851 water molecules. The box dimensions are *3.71233 3.71233 1.85616.* Following are the parameters for the mdp file which I am using: ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling ;Tcoupl = no Tcoupl = nose-hoover tau_t = 2.0 ref_t = 308 tc-grps = system ;Pcoupl = no Pcoupl = Berendsen tau_p = 2.0 pcoupltype = isotropic ref_p = 1 compressibility = 5e-5 I am using *#Surf*SurfTen* option in the g_energy command in GROMACS-4.6.5. I have calculated surface tension for 70 ns NPT run. Following is the output which I am getting: Statistics over 35000001 steps [ 0.0000 through 70000.0000 ps ], 1 data sets All statistics are over 350001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- #Surf*SurfTen -3.53622 2.6 1336.67 0.561131 (bar nm) The value for surface tension of bulk water at 308 K is 70.38 dyn/cm. Kindly tell me whether I am giving some wrong input parameters? Regards, -- *Abhinav Srivastava* *Research Scholar* Indian Institute of Technology, Jodhpur Rajasthan -------------- next part -------------- An HTML attachment was scrubbed... URL: From hess at kth.se Fri Aug 7 10:26:33 2020 From: hess at kth.se (Berk Hess) Date: Fri, 07 Aug 2020 08:26:33 -0000 Subject: [gmx-developers] Surface tension of bulk water In-Reply-To: References: Message-ID: <5661f120-9386-46ff-5cf1-e30e94212048@kth.se> Hi, Please post user questions to the forum: https://gromacs.bioexcel.eu/c/gromacs-user-forum/ But your problem is that you should simulate a box with liquid+gas/vacuum phase so it has interfaces, not bulk liquid. Cheers, Berk On 07/08/2020 10.12, Abhinav Srivastava (P14CHM002) wrote: > Dear Gromacs Users, > > I am trying to calculate the surface tension of bulk water. I am using > TIP4P/2005 water model consisting of 851 water molecules. The box > dimensions are *3.71233 ? 3.71233 1.85616.* > Following are the parameters for the mdp file which I am using: > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > ;Tcoupl ? ? ? ? ? ? ? ? ? = no > Tcoupl ? ? ? ? ? ? ? ? ? = nose-hoover > tau_t ? ? ? ? ? ? ? ? ? ?= 2.0 > ref_t ? ? ? ? ? ? ? ? ? ?= 308 > tc-grps ? ? ? ? ? ? ? ? ?= system > > ;Pcoupl ? ? ? ? ? ? ? ? ? = ?no > > Pcoupl ? ? ? ? ? ? ? ? ? = Berendsen > tau_p ? ? ? ? ? ? ? ? ? ?= 2.0 > pcoupltype ? ? ? ? ? ? ? = isotropic > ref_p ? ? ? ? ? ? ? ? ? ?= 1 > compressibility ? ? ? ? ?= 5e-5 > > I am using *#Surf*SurfTen* option in the g_energy command in > GROMACS-4.6.5. I have calculated surface tension for 70 ns NPT run. > Following is the output which I am getting: > > Statistics over 35000001 steps [ 0.0000 through 70000.0000 ps ], 1 > data sets > All statistics are over 350001 points > > Energy ? ? ? ? ? ? ? ? ? ? ?Average ? Err.Est. ? ? ? RMSD ?Tot-Drift > ------------------------------------------------------------------------------- > #Surf*SurfTen ? ? ? ? ? ? ?-3.53622 ? ? ? ?2.6 ? ?1336.67 0.561131 > ?(bar nm) > > > The value for surface tension of bulk water at 308 K is 70.38 dyn/cm. > > > Kindly tell me whether I am giving some wrong input parameters? > > > Regards, > > > -- > *Abhinav Srivastava* > /Research Scholar/ > Indian Institute of Technology, Jodhpur > Rajasthan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul.bauer.q at gmail.com Wed Aug 12 10:25:42 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Wed, 12 Aug 2020 08:25:42 -0000 Subject: [gmx-developers] developer telco later today Message-ID: <792d67de-72d6-daba-6ba8-3a93b1153fb7@gmail.com> Hi gmx developers! We will have our fortnightly developer roundtable telco later today, at 1700 Stockholm time (CET). Please see the information for the Zoom conferencing setup details below. You can find the password to access the meeting below. Cheers Paul Paul Bauer is inviting you to a scheduled Zoom meeting. Topic: GROMACS Developer bi-weekly videoconference Time: Jun 3, 2020 05:00 PM Stockholm ??????? Every 2 weeks on Wed, 20 occurrence(s) ??????? Jun 3, 2020 05:00 PM ??????? Jun 17, 2020 05:00 PM ??????? Jul 1, 2020 05:00 PM ??????? Jul 15, 2020 05:00 PM ??????? Jul 29, 2020 05:00 PM ??????? Aug 12, 2020 05:00 PM ??????? Aug 26, 2020 05:00 PM ??????? Sep 9, 2020 05:00 PM ??????? Sep 23, 2020 05:00 PM ??????? Oct 7, 2020 05:00 PM ??????? Oct 21, 2020 05:00 PM ??????? Nov 4, 2020 05:00 PM ??????? Nov 18, 2020 05:00 PM ??????? Dec 2, 2020 05:00 PM ??????? Dec 16, 2020 05:00 PM ??????? Dec 30, 2020 05:00 PM ??????? Jan 13, 2021 05:00 PM ??????? Jan 27, 2021 05:00 PM ??????? Feb 10, 2021 05:00 PM ??????? Feb 24, 2021 05:00 PM Please download and import the following iCalendar (.ics) files to your calendar system. Weekly: https://kth-se.zoom.us/meeting/u50rceiuqz8qGdOR67_aLafN5GP3sWF2c0Iv/ics?icsToken=98tyKu-hqD0rHNGRsBqAR_N5BI_od-7wmClfjadyrkmyPCF_YwXYY8VyYaFINorT Join Zoom Meeting https://kth-se.zoom.us/j/69661654037?pwd=VUxPY01qTTFndUoyczhETis1b2F3UT09 Meeting ID: 696 6165 4037 Password: gmxdevs One tap mobile +46850520017,,69661654037# Sweden +46850539728,,69661654037# Sweden Dial by your location ??????? +46 8 5052 0017 Sweden ??????? +46 850 539 728 Sweden ??????? +46 8 4468 2488 Sweden ??????? +46 8 5050 0828 Sweden ??????? +46 8 5050 0829 Sweden Meeting ID: 696 6165 4037 Find your local number: https://kth-se.zoom.us/u/c3IYvf8Dg Join by SIP 69661654037 at zoom.nordu.net From a KTH Cisco Video System you can just input 69661654037 and then the CALL-button Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 696 6165 4037 Password: 586750 -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From smalkaram at wvstateu.edu Sun Aug 23 12:53:21 2020 From: smalkaram at wvstateu.edu (Sridhar Acharya Malkaram) Date: Sun, 23 Aug 2020 10:53:21 -0000 Subject: [gmx-developers] =?windows-1252?q?Retaining_chain_name_and_origin?= =?windows-1252?q?al_residue_numbers__in_=93=2Epdb=94_output_after_mdrun?= In-Reply-To: References: Message-ID: Hi gmx-developers, I had originally posted this in the general mailing list, but without responses. I thought I might get a suggestion here. Any suggestion is appreciated. GROMACS version: 2020.3 GROMACS modification: No I am working on a scripted run of gromacs energy calculation (using gmx energy), to calculate energies for specific groups. I will be specifying in the energygrps option of the mdp to achieve this. However, I find a problem. The original residue numbers and chain names are no longer retained after the series of gromacscommands before the gmx energy command. I am using ?.pdb? as the input and output structure format for my simulation to retain the chain name. Gromacs retains the chain information in output ?.pdb? structures for many of its commands, but when I run mdrun, the output structure file ?.pdb? (the option -c) has lost all chain information. I checked for any options that can be used to preserve chain information, but I found none. I needed chain information in pdb format structure file, to properly generate index groups. Is there a way to preserve chain information? Also, is there a way to prevent residue renumbering ? (Atom renumbering is not an issue) With Kind Regards, Sridhar Sridhar A Malkaram, Ph.D. Associate Professor, Department of Mathematics and Computer Sciences W729, Wallace Hall, West Virginia State University, Institute, WV-25112 Office: +1 (304)-766-5168 -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul.bauer.q at gmail.com Mon Aug 24 08:40:06 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Mon, 24 Aug 2020 06:40:06 -0000 Subject: [gmx-developers] =?utf-8?q?Retaining_chain_name_and_original_resi?= =?utf-8?q?due_numbers_in_=E2=80=9C=2Epdb=E2=80=9D_output_after_mdrun?= In-Reply-To: References: Message-ID: Hello, it is better to ask this stuff at the forum (gromacs.bioexcel.eu) now and maybe repeat the question there, or check if there are similar questions already. This list is only for things related to the GROMACS software development :) If you think that the behavior you describe is a bug, please check the open issues here (https://gitlab.com/gromacs/gromacs/-/issues) if something similar has already been filed and if not open a new issue for it. Cheers Paul On 23/08/2020 12:53, Sridhar Acharya Malkaram wrote: > > Hi gmx-developers, > > I had originally posted this in the general mailing list, but without > responses. I thought I might get a suggestion here. Any suggestion is > appreciated. > > GROMACS?version: 2020.3 > GROMACS?modification: No > > I am working on a scripted run of?gromacs?energy calculation (using > gmx energy), to calculate energies for specific groups. I will be > specifying in the energygrps option of the mdp to achieve this. > However, I find a problem. The original residue numbers and chain > names are no longer retained after the series of?gromacscommands > before ?the gmx energy command. > > I am using ?.pdb? as the input and output structure format for my > simulation to retain the chain name. > > Gromacs?retains the chain information in output ?.pdb? structures for > many of its commands, but when I run mdrun, the output structure file > ?.pdb? (the option -c) has lost all chain information. I checked for > any options that can be used to preserve chain information, but I > found none. > > I needed chain information in pdb format structure file, to properly > generate index groups. > > Is there a way to preserve chain information? > > Also, is there a way to prevent residue renumbering ? (Atom > renumbering is not an issue) > > With Kind Regards, > > Sridhar > > Sridhar A Malkaram, Ph.D. > > Associate Professor, > > Department of Mathematics and Computer Sciences > > W729, Wallace Hall, > > West Virginia State University, > > Institute, WV-25112 > > Office: +1 (304)-766-5168 > > -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul.bauer.q at gmail.com Wed Aug 26 15:38:20 2020 From: paul.bauer.q at gmail.com (Paul bauer) Date: Wed, 26 Aug 2020 13:38:20 -0000 Subject: [gmx-developers] developer telco later today Message-ID: Hi gmx developers! Sorry for almost forgetting this, we will have our fortnightly developer roundtable telco later today, at 1700 Stockholm time (CET). Please see the information for the Zoom conferencing setup details below. You can find the password to access the meeting below. Cheers Paul Paul Bauer is inviting you to a scheduled Zoom meeting. Topic: GROMACS Developer bi-weekly videoconference Time: Jun 3, 2020 05:00 PM Stockholm ??????? Every 2 weeks on Wed, 20 occurrence(s) ??????? Jun 3, 2020 05:00 PM ??????? Jun 17, 2020 05:00 PM ??????? Jul 1, 2020 05:00 PM ??????? Jul 15, 2020 05:00 PM ??????? Jul 29, 2020 05:00 PM ??????? Aug 12, 2020 05:00 PM ??????? Aug 26, 2020 05:00 PM ??????? Sep 9, 2020 05:00 PM ??????? Sep 23, 2020 05:00 PM ??????? Oct 7, 2020 05:00 PM ??????? Oct 21, 2020 05:00 PM ??????? Nov 4, 2020 05:00 PM ??????? Nov 18, 2020 05:00 PM ??????? Dec 2, 2020 05:00 PM ??????? Dec 16, 2020 05:00 PM ??????? Dec 30, 2020 05:00 PM ??????? Jan 13, 2021 05:00 PM ??????? Jan 27, 2021 05:00 PM ??????? Feb 10, 2021 05:00 PM ??????? Feb 24, 2021 05:00 PM Please download and import the following iCalendar (.ics) files to your calendar system. Weekly: https://kth-se.zoom.us/meeting/u50rceiuqz8qGdOR67_aLafN5GP3sWF2c0Iv/ics?icsToken=98tyKu-hqD0rHNGRsBqAR_N5BI_od-7wmClfjadyrkmyPCF_YwXYY8VyYaFINorT Join Zoom Meeting https://kth-se.zoom.us/j/69661654037?pwd=VUxPY01qTTFndUoyczhETis1b2F3UT09 Meeting ID: 696 6165 4037 Password: gmxdevs One tap mobile +46850520017,,69661654037# Sweden +46850539728,,69661654037# Sweden Dial by your location ??????? +46 8 5052 0017 Sweden ??????? +46 850 539 728 Sweden ??????? +46 8 4468 2488 Sweden ??????? +46 8 5050 0828 Sweden ??????? +46 8 5050 0829 Sweden Meeting ID: 696 6165 4037 Find your local number: https://kth-se.zoom.us/u/c3IYvf8Dg Join by SIP 69661654037 at zoom.nordu.net From a KTH Cisco Video System you can just input 69661654037 and then the CALL-button Join by H.323 109.105.112.236 109.105.112.235 Meeting ID: 696 6165 4037 Password: 586750 -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 From isimuly at 163.com Wed Aug 26 20:12:37 2020 From: isimuly at 163.com (isimuly) Date: Wed, 26 Aug 2020 18:12:37 -0000 Subject: [gmx-developers] explanation of gmx rdf Message-ID: <281f23f0.e3.1742bea79f7.Coremail.isimuly@163.com> Hi developers, Recently, I use gmx rdf command to calculate the RDFs. However, I am confused by " -selrpos (atom) Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog -seltype (atom) Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog " what the different res_com, mol_com, part_res_com, mol_cog, and so on? Where could I find some material about their difference? Best Isimuly -------------- next part -------------- An HTML attachment was scrubbed... URL: From spoel at xray.bmc.uu.se Wed Aug 26 21:37:14 2020 From: spoel at xray.bmc.uu.se (David van der Spoel) Date: Wed, 26 Aug 2020 19:37:14 -0000 Subject: [gmx-developers] explanation of gmx rdf In-Reply-To: <281f23f0.e3.1742bea79f7.Coremail.isimuly@163.com> References: <281f23f0.e3.1742bea79f7.Coremail.isimuly@163.com> Message-ID: Den 2020-08-26 kl. 19:57, skrev isimuly: > Hi developers, > > Recently, I use gmx rdf command to calculate the RDFs. However, I am > confused by > " -selrpos ??????????? (atom) > ?????????? Selection reference positions: atom, res_com, res_cog, mol_com, > ?????????? mol_cog, whole_res_com, whole_res_cog, whole_mol_com, > ?????????? whole_mol_cog, part_res_com, part_res_cog, part_mol_com, > ?????????? part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog > ?-seltype ??????????? (atom) > ?????????? Default selection output positions: atom, res_com, res_cog, > ?????????? mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, > ?????????? whole_mol_cog, part_res_com, part_res_cog, part_mol_com, > ?????????? part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog > " > what the different res_com, mol_com, part_res_com, mol_cog, and so on? > Where could I find some material about their difference? > > Best > > Isimuly > > > > > Not a developer question. Please use the forum. https://gromacs.bioexcel.eu/ -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.org