Re: [gmx-users] How to implement LJ 6-12 function form?
I was puzzled by that before, as the LJ interactions by the Lorenzt-Berthelot comb-rules (page 68) looked exactly like the LJ 6-12 function form.Hence I was thinking how can one use the comb-rule type2 (carbon-water nonbond-param) and LJ 6-12 (table6-12.xvg) together. Thank you Eric!Cheers, Kester- 원본 메일 -보낸사람 : Eric Smoll 받는사람 : 받은날짜 : 2014년 10월 29일(수) 10:51:54제목 : Re: [gmx-users] How to implement LJ 6-12 function form?Hello Kester, Setting the first value in the defaults directive to 1 indicates that you want to use the 6-12 LJ potential. As far as I understand, setting N is only necessary if you want the repulsive LJ term to be something other than 12. I don't think you need to do anything else. The first defaults entry looks good. See page 144 of the Gromacs 5.0.2 manual. Best, Eric On Tue, Oct 28, 2014 at 7:40 PM, Kester Wong wrote: > Dear all, > > > I am using GROMACS 5.0, could anyone tell me how can I use the LJ 6-12 in > my calculations? > > My force field [ defaults ] is as follows: > > > [ defaults ] > > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > > 1 2 yes 0.5 0.5 > > > According to the manual, do I add "N" equals to 12 to enable the LJ 6-12 > (carbon-water) interaction parameters to be used, without using the look up > table "table6-12.xvg"? > > > [ defaults ] > > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQN > > LJ 2 yes 0.5 0.5 > 12 > > My current system already has the following parameters bonding, > nonbonding, graphene, water and ions topologies; based on the TIPS3P and > CHARMM27 models. > > Thanks for any input! > > Regards, > Kester > > > > -- > 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. > > -- 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. -- 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] How to implement LJ 6-12 function form?
Hello Kester, Setting the first value in the defaults directive to 1 indicates that you want to use the 6-12 LJ potential. As far as I understand, setting N is only necessary if you want the repulsive LJ term to be something other than 12. I don't think you need to do anything else. The first defaults entry looks good. See page 144 of the Gromacs 5.0.2 manual. Best, Eric On Tue, Oct 28, 2014 at 7:40 PM, Kester Wong wrote: > Dear all, > > > I am using GROMACS 5.0, could anyone tell me how can I use the LJ 6-12 in > my calculations? > > My force field [ defaults ] is as follows: > > > [ defaults ] > > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > > 1 2 yes 0.5 0.5 > > > According to the manual, do I add "N" equals to 12 to enable the LJ 6-12 > (carbon-water) interaction parameters to be used, without using the look up > table "table6-12.xvg"? > > > [ defaults ] > > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQN > > LJ 2 yes 0.5 0.5 > 12 > > My current system already has the following parameters bonding, > nonbonding, graphene, water and ions topologies; based on the TIPS3P and > CHARMM27 models. > > Thanks for any input! > > Regards, > Kester > > > > -- > 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. > > -- 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 implement LJ 6-12 function form?
Dear all, I am using GROMACS 5.0, could anyone tell me how can I use the LJ 6-12 in my calculations?My force field [ defaults ] is as follows:[ defaults ]; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 2 yes 0.5 0.5According to the manual, do I add "N" equals to 12 to enable the LJ 6-12 (carbon-water) interaction parameters to be used, without using the look up table "table6-12.xvg"?[ defaults ]; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ NLJ 2 yes 0.5 0.5 12My current system already has the following parameters bonding, nonbonding, graphene, water and ions topologies; based on the TIPS3P and CHARMM27 models.Thanks for any input!Regards,Kester -- 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] pdb2gmx
Hello Gromacs users, I would like to add a molecule as a "residue" in the aminoacids.rtp file and I have a few questions. As far as I understand, a residue in a gro file can multiple atoms with the same "atom name." What links every atom in this residue to parameters in the top [ atoms ] directive is the *order.* The gro file "atom names" must match the top file atoms names but the mapping of parameters is done via the order, correct? This allows atoms in a residue to have the same "atom name" but be associated with a different "atom type," "charge group," etc... Does an entry in a residue database (e.g., aminoacids.rtp) work the same way? The syntax is shown below. [ TEST ] [ atoms ] ; atom_nameatom_typeatom_chargecharge_group I have to specify the "atom name," force field "atom type," "atom charge," and "charge group" for every atom in the "TEST" residue in order. The "atom name" must match the "atom name" in the input coordinate file but the mapping is applied by the entry order, correct? I do no need unique "atom names," correct? Best, Eric -- 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] Free energy in implicit solvent
Dear gromacs users, Is it possible to calculate free energy in implicit solvent in gromacs? -- 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] combine tpr files?
On 10/28/14 3:24 PM, Urszula Uciechowska wrote: Dear Gromacs users, I am following the tutorial: http://www3.nd.edu/~gezelter/Teaching/650/exercises/gromacs/ and I want to use the command: g_rama -f ../full.trr -s ../full.tpr -o rama.xvg - I was wondering how to get the full.tpr file? is there any command to cat those files? I run MD for 50ns and I was extending my simulations every 10ns. You do not need to concatenate .tpr files. Analysis tools use the contents of .tpr files in various ways, sometimes just for names, masses, charges, etc. Some programs need a reference coordinate file, and the coordinates can be taken from a .tpr file. If you've been doing your simulations in chunks of 10 ns by extending via tpbconv, the contents of each of your .tpr files are identical except for the number of steps. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Silica monolayer with Martini force field
Hi Gromacs users, I want to simulate a monolayer of alkane molecules attached to a solid glass surface. I wonder if anyone has experience with these kinds of systems with the Martini force field. My idea is to add water to the surface and I am interested in what happens between water and the fixed alkanes, so I will freeze the solid beads and the first carbon of the alkane chain. My question is what kind of beads would correspond to glass (silica) surface? Somewhere I found that 'Na' beads could be used to simulate a Pt surface, but I do not know if this would work in my case. Did anyone has experience simulating solid surfaces with Martini? thank you, Ramon Aquest correu electr?nic i els annexos poden contenir informaci? confidencial o protegida legalment i està adreçat exclusivament a la persona o entitat destinatària. Si no sou el destinatari final o la persona encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu rebut aquest correu electr?nic per error, us preguem que n’informeu al remitent i que elimineu del sistema el missatge i el material annex que pugui contenir. Gràcies per la vostra col·laboraci?. Este correo electr?nico y sus anexos pueden contener informaci?n confidencial o legalmente protegida y est? exclusivamente dirigido a la persona o entidad destinataria. Si usted no es el destinatario final o la persona encargada de recibirlo, no est? autorizado a leerlo, retenerlo, modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha recibido este mensaje electr?nico por error, le rogamos que informe al remitente y elimine del sistema el mensaje y el material anexo que pueda contener. Gracias por su colaboraci?n. This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. -- 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] combine tpr files?
Dear Gromacs users, I am following the tutorial: http://www3.nd.edu/~gezelter/Teaching/650/exercises/gromacs/ and I want to use the command: g_rama -f ../full.trr -s ../full.tpr -o rama.xvg - I was wondering how to get the full.tpr file? is there any command to cat those files? I run MD for 50ns and I was extending my simulations every 10ns. Any suggestions? best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] Calculating intermolecular energies of water
I am writing a routine in C, to calculate the energy of intermolecular interactions of water in a nano cavity, at each time step. There is variable number of waters per each simulation step. I am using the system() function, to repeat the following calls to gromacs over and over. 1) g_select (To make an index file of waters at time step i) 2) trjconv (To get positions of water at time step i) 3) tpbconv (To make *.tpr file for pore water at time step i) 4) mdrun -rerun (To get *.edr file) 5) g_energy (To calculate short range LJ and Coulomb interaction) Would this give me intermolecular interaction energies without having to make a group in an *.mdp file? Or am I going to have perform grompp instead of tpbconv? On Oct 28, 2014, at 11:27 AM, David van der Spoel wrote: > On 2014-10-28 18:12, Jackson Chief Elk wrote: >> Hi, >> When using g_energy to calculate short-range Coulomb interactions between a >> dynamically sized group of water, made with g_select, does the output >> contain both bonded and non bonded contributions? >> Jackson >> > I don't think this is possible at all. You need to define energy groups > before your simulation. > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > 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. -- 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] The last line in a .gro file
If the PDB file has a CRYST1 record, then there is a box, and it is converted to GRO format by pdb2gmx. Tsjerk On Tue, Oct 28, 2014 at 6:46 PM, Mark Abraham wrote: > Probably. Try a differently sized molecule ;-) > > Mark > > On Tue, Oct 28, 2014 at 5:58 PM, Agnivo Gosai > wrote: > > > Dear Users > > > > The last line of the .gro file lists out three co-ordinates and the > GROMACS > > manual says that these are the box vectors : v1(x) , v2(y) and v3(z) > > Now , before using editconf to place our molecule inside a box , there is > > no box associated with the system. > > But pdb2gmx generates this .gro file having the vectors listed in the > last > > line. > > > > My question is :- Is the last line has to do anything with the "size" of > > the molecule ? > > > > Thanks & Regards > > Agnivo Gosai > > Grad Student, Iowa State University. > > -- > > 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. > > > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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] The last line in a .gro file
Probably. Try a differently sized molecule ;-) Mark On Tue, Oct 28, 2014 at 5:58 PM, Agnivo Gosai wrote: > Dear Users > > The last line of the .gro file lists out three co-ordinates and the GROMACS > manual says that these are the box vectors : v1(x) , v2(y) and v3(z) > Now , before using editconf to place our molecule inside a box , there is > no box associated with the system. > But pdb2gmx generates this .gro file having the vectors listed in the last > line. > > My question is :- Is the last line has to do anything with the "size" of > the molecule ? > > Thanks & Regards > Agnivo Gosai > Grad Student, Iowa State University. > -- > 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. > -- 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] Calculating intermolecular energies of water
On Tue, Oct 28, 2014 at 6:27 PM, David van der Spoel wrote: > On 2014-10-28 18:12, Jackson Chief Elk wrote: > >> Hi, >> When using g_energy to calculate short-range Coulomb interactions between >> a dynamically sized group of water, made with g_select, does the output >> contain both bonded and non bonded contributions? >> Jackson >> >> I don't think this is possible at all. You need to define energy groups > before your simulation. Indeed. But if Jackson meant to ask about short-range Coulomb, then bonded contributions do not apply. Nor would they if the water model was rigid, as is typically the case. Mark > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > > -- > 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. > -- 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] Calculating intermolecular energies of water
On 2014-10-28 18:12, Jackson Chief Elk wrote: Hi, When using g_energy to calculate short-range Coulomb interactions between a dynamically sized group of water, made with g_select, does the output contain both bonded and non bonded contributions? Jackson I don't think this is possible at all. You need to define energy groups before your simulation. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Calculating intermolecular energies of water
Hi, When using g_energy to calculate short-range Coulomb interactions between a dynamically sized group of water, made with g_select, does the output contain both bonded and non bonded contributions? Jackson -- 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] The last line in a .gro file
Dear Users The last line of the .gro file lists out three co-ordinates and the GROMACS manual says that these are the box vectors : v1(x) , v2(y) and v3(z) Now , before using editconf to place our molecule inside a box , there is no box associated with the system. But pdb2gmx generates this .gro file having the vectors listed in the last line. My question is :- Is the last line has to do anything with the "size" of the molecule ? Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] How fshift array works?
On 2014-10-28 16:41, jia jia wrote: Dear Gromacs users: Has anyone got idea how "fshift" array in src/gmxlib/bondfree.c works? I'm modifing this part to add some new function but could not figure out what's the function of it. For exemple, in a common bond potential for atom i and j, it normally end like fshift[ki][m] += fij; fshift[CENTRAL][m] -= fij; I could not find information about this narray in manual and wonder has any one have some idea about it. Thank you very much! Yours Guang It's in the manual. Look for calculation of virial. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Martini + Elnedyn
Hi Tsjerk, Thanks for your reply. yes, I will do a test and then I will be ready to more questions ;-) Best Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** 2014-10-28 16:04 GMT+01:00 Tsjerk Wassenaar : > Hi Adriana, > > By default, with martinize, the elastic network will be applied to each > chain separately. You'll need to explicitly merge chains to have a network > between two chains. So you should be fine following the tutorial like that. > > Best, > > Tsjerk > > On Tue, Oct 28, 2014 at 3:01 PM, Adriana Garro > wrote: > > > Dear Gromacs users, > > > > I am interested in apply Martini + Elnedyn to my system so I followed the > > tutorial: > > > > http://md.chem.rug.nl/cgmartini/index.php/proteins#elnedyn > > > > and it works well, now I am using the same script provided by the > tutorial > > but as my system is different (I am trying to use TMD as well) I would > > need to perform some modifications, for example I dont want elastic > > network between the 2 molecules because they are not different chains of > > the same macromolecule like in the tutorial so my question is: is it > > possible to use in the same box 2 differents networks one to each > molecule? > > Can someone suggest some tutorial or paper related to this topic? > > Thanks in advance. > > Best, > > > > Adriana > > -- > > 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. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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. > -- 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 fshift array works?
Dear Gromacs users: Has anyone got idea how "fshift" array in src/gmxlib/bondfree.c works? I'm modifing this part to add some new function but could not figure out what's the function of it. For exemple, in a common bond potential for atom i and j, it normally end like fshift[ki][m] += fij; fshift[CENTRAL][m] -= fij; I could not find information about this narray in manual and wonder has any one have some idea about it. Thank you very much! Yours Guang -- 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] Martini + Elnedyn
Hi Adriana, By default, with martinize, the elastic network will be applied to each chain separately. You'll need to explicitly merge chains to have a network between two chains. So you should be fine following the tutorial like that. Best, Tsjerk On Tue, Oct 28, 2014 at 3:01 PM, Adriana Garro wrote: > Dear Gromacs users, > > I am interested in apply Martini + Elnedyn to my system so I followed the > tutorial: > > http://md.chem.rug.nl/cgmartini/index.php/proteins#elnedyn > > and it works well, now I am using the same script provided by the tutorial > but as my system is different (I am trying to use TMD as well) I would > need to perform some modifications, for example I dont want elastic > network between the 2 molecules because they are not different chains of > the same macromolecule like in the tutorial so my question is: is it > possible to use in the same box 2 differents networks one to each molecule? > Can someone suggest some tutorial or paper related to this topic? > Thanks in advance. > Best, > > Adriana > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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] Martini + Elnedyn
Dear Gromacs users, I am interested in apply Martini + Elnedyn to my system so I followed the tutorial: http://md.chem.rug.nl/cgmartini/index.php/proteins#elnedyn and it works well, now I am using the same script provided by the tutorial but as my system is different (I am trying to use TMD as well) I would need to perform some modifications, for example I dont want elastic network between the 2 molecules because they are not different chains of the same macromolecule like in the tutorial so my question is: is it possible to use in the same box 2 differents networks one to each molecule? Can someone suggest some tutorial or paper related to this topic? Thanks in advance. Best, Adriana -- 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] question about walls for a simple water box
Dear Gromacs users, I am following the tutorial: http://www3.nd.edu/~gezelter/Teaching/650/exercises/gromacs/ and I want to use the command: g_rama -f ../full.trr -s ../full.tpr -o rama.xvg - I was wondering how to get the full.tpr file? is there any command to cat those files? I run MD for 50ns and I was extending my simulations every 10ns. Any suggestions? best regards Urszula Uciechowska --- University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] question about walls for a simple water box
Dear Gromacs users, Unfortunately I am failing with the use of the wall options using martini force field simulations. However, I still want to make the last attempt to work with walls. The example is simple, I built a water box with 1000 water molecules, I minimized possible contacts (steep) and then I run a constant isotropic pressure (1bar) equilibration. I checked that he water density is the correct one (about 1000 gr/l) and then I tred to simulate the water box with pbc = xy, No pressure and walls in z=0 and z=zbox. I set the wall_atomtypes to an alkane carbon bead (C1 in the martini force field) and try 9-3, 10-4 and 12-6 potentials with different values of wall_rlin (1, 10, 10…). I use ewald summations for the electrostatic interactions and I set ewald_geometry =3dc and wall_ewald_zfac=3. See the mdp below. In all the attemps, the water box broke in two pieces and water escapes to large positive or negative z values outside the initial water box. could anyone tell me what is the problme with this simple simulation? thanks, Ramon ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0.0 dt = 0.0200 nsteps = 20 ; number of steps for center of mass motion removal = nstcomm = 1 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 2000 nstvout = 2000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 2000 nstenergy= 2000 ; Output frequency and precision for xtc file = nstxtcout= 2000 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = W ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xy nwall = 2 wall_atomtype = C1 C1 wall_type = 9-3 wall_density = 110 110 wall_r_linpot = 1 1 wall_ewald_zfac = 3 ; nblist cut-off = rlist= 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths= rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 10 fourier_ny = 10 fourier_nz = 10 ; EWALD/PME/PPPM parameters = pme_order= 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ewald_geometry = 3dc ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = W ; Time constant (ps) and reference temperature (K) = tau_t= 1.0 ref_t= 310 ; Pressure coupling = Pcoupl = No Aquest correu electrònic i els annexos poden contenir informació confidencial o protegida legalment i està adreçat exclusivament a la persona o entitat destinatària. Si no sou el destinatari final o la persona encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu rebut aquest correu electrònic per error, us preguem que n’informeu al remitent i que elimineu del sistema el missatge i el material annex que pugui contenir. Gràcies per la vostra col·laboració. Este correo electrónico y sus anexos pueden contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no es el destinatario final o la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha recibido este mensaje electrónico por error, le rogamos que informe al remitente y elimine del sistema el mensaje y el material anexo que pueda contener. Gracias por su colaboración. This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle
On 10/28/14 6:23 AM, Björn Sommer wrote: Dear Rajat, Dear Andre, Dear all, thanks again for your help. 1) I'm simulating an united atoms model and isotropic pressure is used, not coarse-grained (this would be indeed more simple, because faster and much more examples are available). 2) Yes, I added additional water bubbles of different sizes only in the vacuum region. 3) I don't know the lateral tension yet, but I'll try to compute it and hand in this information later. 4) Do you have sufficient water outside the vesicle to hydrate all the lipids in the outer leaflet? 4) Yes, there should be enough water. I think, that this is currently not the problem, but we will keep this in mind. In addition, you find two snapshots, one of the vacuum bubble and one of the inner lipid layer coated by water: http://www.CELLmicrocosmos.org/images/downloads/cm2/WANTED_vacuum_bubble.pdf (Sorry, I just had to do this joke, Manuel! - Björn ;-) In addition I'm running a minimization run right now with a lot more water inside and will continue to equillibrate soon, as far as I get an useful result, we will inform you. Does the size of the vesicle itself change at all? My thought is that this could simply be a force field issue; if the surface tension in the vesicle is wrong, then if it gets larger over time, there's only a finite amount of water in the center of the vesicle, so bubbles develop. Apologies if I've missed relevant information; I've been following the thread but have not had time to study it very closely. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] error in the middle of running mdrun_mpi
On 10/28/14 7:16 AM, Nizar Masbukhin wrote: Now, the only thing worrying me is a warning "Turning off pressure coupling for vacuum system" on NPT equilibration. Can I just ignore this warning or should i do something? as i didn't mean my system in vacuum. You can't do NPT with pbc = no, as your earlier .mdp files showed, so nothing can be scaled. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] error in the middle of running mdrun_mpi
Now, the only thing worrying me is a warning "Turning off pressure coupling for vacuum system" on NPT equilibration. Can I just ignore this warning or should i do something? as i didn't mean my system in vacuum. -- 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] error in the middle of running mdrun_mpi
Thank you very much Justin and Mark. On Tue, Oct 28, 2014 at 2:31 AM, Mark Abraham wrote: > On Mon, Oct 27, 2014 at 6:05 PM, Nizar Masbukhin > wrote: > > > i dont really understand the point. could you please what do you mean in > > the last reply? > > what command should i use? > > > > if, say i have 72 cores in 9 nodes, and 16 replicas to simulate in > implicit > > solvent. > > > Hi, > > You can only use two MPI ranks per replica if there's a limit of two ranks > per simulation. So that's 32 ranks total. So something like > > mpirun -np 32 mdrun_mpi -multidir -repl_ex whatever > > after setting up the MPI environment to fill four nodes. > > Mark > -- > 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. > -- Thanks My Best Regards, Nizar Medical Faculty of Brawijaya University -- 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] Naughty Vacuum Bubble in our Vesicle
Dear Rajat, Dear Andre, Dear all, thanks again for your help. 1) I'm simulating an united atoms model and isotropic pressure is used, not coarse-grained (this would be indeed more simple, because faster and much more examples are available). 2) Yes, I added additional water bubbles of different sizes only in the vacuum region. 3) I don't know the lateral tension yet, but I'll try to compute it and hand in this information later. 4) Do you have sufficient water outside the vesicle to hydrate all the lipids in the outer leaflet? 4) Yes, there should be enough water. I think, that this is currently not the problem, but we will keep this in mind. In addition, you find two snapshots, one of the vacuum bubble and one of the inner lipid layer coated by water: http://www.CELLmicrocosmos.org/images/downloads/cm2/WANTED_vacuum_bubble.pdf (Sorry, I just had to do this joke, Manuel! - Björn ;-) In addition I'm running a minimization run right now with a lot more water inside and will continue to equillibrate soon, as far as I get an useful result, we will inform you. Best wishes, Manuel and Björn -- 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.
