Re: [gmx-users] Tables - two non-bonded interactions
Hello I think the easiest way to do this is to use multiple tables. Look at: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials There are some details there. ciao Gareth 2011/3/22 Vinícius Contessoto vinicius...@yahoo.com.br: hello! I trying to simulate a protein with C-alpha model (my protein have only alpha-carbons) . I need two different interatomic interactions. 1 - Some interactions in a specific alpha-carbons, using a Lennard Jones 10 -12 potential (i'm determining the pairs in my topology file). 2 - All carbons in my system should to interact among themselves with a Buckingham potential ( here is the problem - how can i use this potential for all my atoms and a LJ 10-12 to just a few atoms?) I'm using a table for a LJ 10-12 and trying to use a table to Buckingham. Thank You! -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tabulated potentials and normal nonbonded interaction at the same time
Hello I think what you need to do is use multiple tables. So you have one table for your CG-solvent interaction with itself and then another one for your CG-solvent (uncharged) interactions. (This second table would then just a tabulated version of the Lennard Jones interaction or whatever you are using.) This page might be of help: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials ciao Gareth On Wed, Sep 15, 2010 at 5:40 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Dear Gromacs-User, i want to try to simulate an atomistic molecule with CG-solvent (uncharged). For the atomistic molecule i want to use the normal non-bonded interactions, but for the CG-solvent interaction with itself and the molecule i need a tabulated potential. So my question is, is that possible to do in Gromacs? I looked a little bit into the manual and it seems that tabulated potentials use the 'vdw_type' and/or the 'coulomb_type' keyword, which i will need for the normal interactions. Greetings Thomas -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Tabulated potentials
Hi I think this is what you need to do: (1) Ensure that the topol.top and index.ndx files are set up in the manner described on the wikki. (2) Put in the mdp file the following: energygrps = A B C energygrp_table = A C B B B C (3) Now create a set of files as follows table.xvg - containing the A B interactions table_A_C.xvg - containing the A C interactions table_B_B.xvg - containing the B B interactions table_B_C.xvg - containing the B C interactions You now run with mdrun -table table.xvg gromacs will read in all these files as energygrp_table tells it that it must read table_A_C.xvg, table_B_B.xvg and table_B_C.xvg as well as table.xvg. To put this all another way, when you use the command vdw-type = user (incidentally I think you said that there are no electrostatics so you can use coulombtype = cut-off as it will make no difference) Then you have to provide a table file with definitions of f(r), g(r) and h(r). Then gromacs it will use this table for all the non-bonded interactions (so in your case AA, AB, AC, BB, BC and CC interactions). However, when you add: energygrp_table = A C Then you are saying, oh but please do something different for A C interactions, do what is in the table_A_C.xvg file instead. As a side note, correct me if I am wrong, but there are no AA or CC interactions in your molecule? With the set up I describe above they would have a functional form equivalent to the A B interaction. This is obviously not important if their parameters are equal to zero. Finally, if your still not sure that stuff has been read in you can look in the log file, which should say what tables have been read in. It will also give you warnings (although these maybe in standard error I can't remember) if your tables are not set up properly. ciao Gareth On Tue, Apr 20, 2010 at 7:38 PM, Martin Vartorelli mrvartore...@gmail.comwrote: Hi Gromacs users, previously I've posted my situation with a simulation and I'm still confused: I have 3 groups of different atoms: A, B and C, and tabulated bonding and non-bonding potentials. The tabulated bonded potentials are specified in the files: table_b1.xvg table_a1.xvg table_a2.xvg table_a3.xvg Because the systems is simply this molecule: A--(B)n--C, the *.mdp file contains the following: coulombtype = user vdw-type= user energygrps = A B C energygrp_table = A B A C B B B C From the manual and tutorials I understand that, for the non bonding part of U, I can suply a file called table.xvg that contains the 7 non-zero columns for r, f, f', g, g', h and h'. The file table.xvg must contain the functions for AB interactions and the remaining interactions must be in the files table_A_C.xvg, table_B_B.xvg and table_B_C.xvg. So, in the command line I can write: mdrun -table table.xvg -tableb table I'm right? As a test I have also included the file table_A_B.xvg (the same potential functions that table.xvg) in the same directory, and when I look at the log file it shows that this file is readed too. I'm still unclear... how must I specify the files in an univocal way for the non bonding interactions that I want? Gromacs version: 4.0.7 Any help will be appreciated. Martin. PD: I've received some private e-mails explaining to me some issues about spam, mailing lists, private mails, etc. Thanks to all and I apologize if I've bother someone, it wasn't my intention. And for those who spontaneously shows me their support, I don't want it and I don't need it! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with tabulated potentials for 3 different atoms
Dear Martin As Mark has already told you - if you have a problem with gromacs email the list and wait for a reply. Don't just email people you don't know from Adam and expect them to reply because you are in a rush. The file that you have read from the mailing list contains everything I know about tabulated potentials in gromacs. I can't say I fully understand your email but I think that your questions (other than the stuff on bonded potentials) are all covered on the wikki page and certainly are covered in the pdf file I wrote. In short For the bonding part I have the following table files: table_b1.xvg table_a1.xvg table_a2.xvg table_a3.xvg I know nothing about using tabulated potentials for bonded interactions. If this is what is in the manual though its probably right. Must I write energygrps = A B C energygrp_table = AC BB BC in the mdp file and use the tables table.xvgThis has the A B interaction in? table_A_C.xvg table_B_B.xvg table_B_C.xvg with the command line for mdrun saying -table table.xvg? Yes this is exactly what the wikki tells you to do. Why do you think it wont work in your case? Incidentally, you can work out if this is working by doing one md step in gromacs and comparing the energy you obtain with the energy you get from another code, which you are confident produces correct energies. Another thing, because the tables doesn't have to contain only zero columns... Can I put anything on the f and f' columns (because the charge of my atoms is zero)? Yes. I always use f=1/r even though I know it will be ignored (with this choice f'=1/r**2 obviously) Can I put (for example) 0.5 in the g and g' columns and my potential (and the force) minus 0.5 in columns h and h'? I don't understand what you want to do here. If you put 0.5 in g then g'=0, which you can work out using, what I assume, is the first thing you learnt about calculus. ciao Gareth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topology and force fields
Hello I think what you have been told is wrong. You need to include both ffcharmm27.itp and tip3p.itp as the atomtypes in your tip3p.itp will otherwise not be defined. There is an easy way to check though - take out the include ffcharmm27.itp and try to run grompp on your new topology. My bet would be that it won't work and, if you are using rigid molecules, it will tell you that it finds a settles section in the wrong place. ciao Gareth On Mon, Apr 5, 2010 at 7:26 PM, Lum Nforbi lumngwe...@gmail.com wrote: Hello all, Below are the contents of a water1.top file that I used to simulate 2000 molecules of TIP3P water (NPT). I made this topology file according to the pattern on page 114 of the manual (topology for Urea in water). My diffusion coefficient, viscosity and radial distribution functions matched those for tip3p water in literature. Recently I was told that I did not need to use another force field in the topology like ffcharmm27.itp since tip3p.itp is already a forcefield on its own. Could this be true? I just wanted to verify the authenticity of my simulation. If the structure of the topology below is not correct, please let me know. ; The force field files to be included #include ffcharmm27.itp ; Include TIP3P water topology #include tip3p.itp [ system ] Pure Water [ molecules ] ;molecule name number SOL 1936 SOL64 I appreciate your answers. Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Potential Tables for user defined potentials
Hi all I have just been stuck on this very problem of user defined potentials. When I emailed this list I was asked if I could make notes on the solution as this is a problem that seems to come up a lot. Anyway, I will send the notes to you separately Sikandar and would ask if anyone knows where should put/send them if they are to be accessible to the user community? Many thanks Gareth On Sun, Apr 4, 2010 at 3:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sikandar Mashayak wrote: Hi I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that I need to use custom potential field parameters for fluid-fluid and fluid-wall interactions. So my question is that, how can I use potential table approach to specify fluid-fluid and fluid-wall interactions seperately? Start with the manual, section 6.7.2, and see the table*.xvg in the /share/top subdirectory of your Gromacs installation for examples. -Justin Thanks sikandar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] custom forcefields or a new forcefields
Hi Basically you can provide a file in which you calculate the values of your potential function for different values of r. You will have to write a small program to create the table file yourself I think. The details of what should be in it are described in section 6.7.2 of the manual but briefly gromacs treats your forcefield as follows: V(r) = (q_i q_j / 4 pi eps_0 ) f(r) + A g(r) + C h(r) Your table should have seven columns which are: r, f(r) , f'(r) , g(r), g'(r) , h(r), h'(r) Gromacs will then get itself the A and C from the topol.top file. (incidentally your mix type in the initial defaults line should be 1). The spacing between r values will depend on whether you are using a single or double precision version of gromacs. As an example if you were using Lennard Jones with a coulomb interaction f(r) = 1/r g(r) = -1/r**6 h(r) = 1/r**12 You then need to put the tables you are using in the directory in which you are running gromacs. Ciao Gareth On Thu, Apr 1, 2010 at 12:08 PM, DreamCatcher huangshuping1...@gmail.comwrote: Message: 5 Date: Thu, 01 Apr 2010 16:30:44 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] custom forcefields or a new forcefields To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bb42f84.9050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 01/04/10 16:20, DreamCatcher wrote: Hello gmx-users, I have just look through the mail-list to find this http://lists.gromacs.org/pipermail/gmx-users/2009-October/045569.htmlconcerned on the develop of a new force field. It seems that If I wanna use a force field haven't been incooperate into the gromacs' extant version, What I need to do only is to make some new files with suffixes like .rtp / .hdb / nb.itp / bon.itp to contain the new force field parameters. Yes. This may certainly work out for pdb2gmx programme, But will it also work out for another programmes like mdrun? Well, it will, because pdb2gmx builds topologies that grompp can parse into input for mdrun. Cause maybe the forcefield potential function are different from any other forcefileds contained in the gromacs. Then what others can I do to finally introduce a totally new force field to gromacs? Have a look at all the possibilities GROMACS already knows about in chapter 4, and consider also the use of table-lookups for two-body functions (manual 6.7.2). IIRC many-bodied functions won't work yet. Mark -- Hey Mark, Thanks very much for your benevolence. Another question, How can I set up a new functions? Where should they be located? What do you mean when you talk about table-lookups for two-body functions? Where should the lookups take place? When I use man mdrun to find a -table option for table-lookup, it obviously indicates an input file **.xvg, What can **.xvg file do? How should it be created? What is the content in it? Thank a lot and thanks in advance! celeste 2010-4-1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] custom forcefields or a new forcefields
Oh almost forgot you also have to put vdw-type = user in the mdp file. As this tell gromacs to read in the tables. Gareth On Thu, Apr 1, 2010 at 3:25 PM, Gareth Tribello gareth.tribe...@gmail.comwrote: Hi Basically you can provide a file in which you calculate the values of your potential function for different values of r. You will have to write a small program to create the table file yourself I think. The details of what should be in it are described in section 6.7.2 of the manual but briefly gromacs treats your forcefield as follows: V(r) = (q_i q_j / 4 pi eps_0 ) f(r) + A g(r) + C h(r) Your table should have seven columns which are: r, f(r) , f'(r) , g(r), g'(r) , h(r), h'(r) Gromacs will then get itself the A and C from the topol.top file. (incidentally your mix type in the initial defaults line should be 1). The spacing between r values will depend on whether you are using a single or double precision version of gromacs. As an example if you were using Lennard Jones with a coulomb interaction f(r) = 1/r g(r) = -1/r**6 h(r) = 1/r**12 You then need to put the tables you are using in the directory in which you are running gromacs. Ciao Gareth On Thu, Apr 1, 2010 at 12:08 PM, DreamCatcher huangshuping1...@gmail.comwrote: Message: 5 Date: Thu, 01 Apr 2010 16:30:44 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] custom forcefields or a new forcefields To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4bb42f84.9050...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 01/04/10 16:20, DreamCatcher wrote: Hello gmx-users, I have just look through the mail-list to find this http://lists.gromacs.org/pipermail/gmx-users/2009-October/045569.htmlconcerned on the develop of a new force field. It seems that If I wanna use a force field haven't been incooperate into the gromacs' extant version, What I need to do only is to make some new files with suffixes like .rtp / .hdb / nb.itp / bon.itp to contain the new force field parameters. Yes. This may certainly work out for pdb2gmx programme, But will it also work out for another programmes like mdrun? Well, it will, because pdb2gmx builds topologies that grompp can parse into input for mdrun. Cause maybe the forcefield potential function are different from any other forcefileds contained in the gromacs. Then what others can I do to finally introduce a totally new force field to gromacs? Have a look at all the possibilities GROMACS already knows about in chapter 4, and consider also the use of table-lookups for two-body functions (manual 6.7.2). IIRC many-bodied functions won't work yet. Mark -- Hey Mark, Thanks very much for your benevolence. Another question, How can I set up a new functions? Where should they be located? What do you mean when you talk about table-lookups for two-body functions? Where should the lookups take place? When I use man mdrun to find a -table option for table-lookup, it obviously indicates an input file **.xvg, What can **.xvg file do? How should it be created? What is the content in it? Thank a lot and thanks in advance! celeste 2010-4-1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using lennard jones and buckingham terms simultaneously
Hello again Still trying to get this carbonate forcefield to work with gromacs. I now know that the tables and so on are being read in correctly as I can get gromacs to reproduce the energies that I get for the various terms when I calculate them by hand/with a separate program. There is stilla a problem with the charge groups however. As when I attempt to split up the atoms in the water molecule the simulation fails. Again checking that I am doing this correctly I would replace: ; at type res nr res name at name cg nr charge mass 1 amber99_61 1 SOL OW1 0 16.0 2 amber99_60 1 SOL HW21 0.52422 1.00800 3 amber99_60 1 SOL HW31 0.52422 1.00800 4 MW 1 SOL MW4 1 -1.04844 0.0 with ; at type res nr res name at name cg nr charge mass 1 amber99_61 1 SOL OW1 0 16.0 2 amber99_60 1 SOL HW22 0.52422 1.00800 3 amber99_60 1 SOL HW33 0.52422 1.00800 4 MW 1 SOL MW4 4 -1.04844 0.0 The problem I get (even if I just run water without any carbonate/tabulated potentials) if I do the above is that the settles algorithm fails. I'm obviously missing something fundamental - I'm not even sure that cg nr stands for the charge group. Any help would be greatly appreciated. Gareth On Thu, Mar 25, 2010 at 11:07 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/03/2010 7:03 AM, Gareth Tribello wrote: Hello again I have tried to do as you suggest and use tables but I have a new problem. First let me describe my process and then you can let me know if there is anything wrong in the stages: OK so first you include the following directives into the mdp file: coulombtype = pme (or whatever sort of coulomb interaction you are using) vdw-type = user energygrps = Ca CCA OCA OW HW energygrp_table = Ca OCA Ca CCA OCA OCA OCA OW OCA HW Gromacs is then (at some stage) going to look for a series of files called table.xvg - which is the default 6-12 Lennard Jones that will be used for most of the atoms table_Ca_OCA.xvg - which are the Buckingham interactions between your various atom types. table_Ca_CCA.xvg table_OCA_OCA.xvg table_OCA_OW.xvg table_OCA_HW.xvg These files have the format (and contents) described in section 6.7 of the manual. Finally, you define the various energy groups Ca, OCA and so on in your index.ndx file. The problem is that grompp gives me the following error: atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in different energy groups (incidentally these atoms 1 and 2 are OW and HW) Does this mean that I cannot use different tabulated potentials for different atoms in a molecules? By which I mean that I can't use different tabulated potentials for the OW Ca and HW Ca interactions for example? Charge groups are the fundamental unit GROMACS uses in constructing a simulation. Energy groups are the next higher layer in the data structures, and these must be sets of whole charge groups. With some electrostatics models, looping over charge groups whose charge is preferably an integer is essential for modelling correct behaviour. GROMACS does a complex sorting of all the interactions between charge groups into lists that allow it to iterate over charge groups and energy groups. A user table then gets applied to a whole intra- or inter- energy-group loop. Thus your attempt violates this precondition. However, PME does not require the use of charge groups for accurate results, since all inter-atomic electrostatic interactions get treated, regardless of distance. So you could decompose your water molecules into two charge groups, O and Hs. (Caveat, a near-brokenly bad PME approximation might get a little worse with arbitrary charge groups) Final question, as its not clear to me from the manual, if you use a tabulated potential for Lennard Jones and you use mix type 2 (so are you are providing epsilon and sigma in the input rather than A and B) does gromacs still know that it has to manipulate the input parameters in order to get the coefficients of the (tabulated) g(r) and h(r) dispersion and repulsion functions (I mean the g(r) and h(r) defined in section 6.7 of the manual here)? At the same time does it also know not to do anything to the parameters you input for the (tabulated) buckingham potentials (as for a buckingham you are providing A and C)? I expect the point of the tables is that GROMACS just uses them per equation 6.23. Thus I'd expect C6 and C12 in that equation to be constructed according to whatever combination rule is in force. If you've specified them explicitly in the topology (see chapter 5
Re: [gmx-users] Using lennard jones and buckingham terms simultaneously
Hello again I have tried to do as you suggest and use tables but I have a new problem. First let me describe my process and then you can let me know if there is anything wrong in the stages: OK so first you include the following directives into the mdp file: coulombtype = pme (or whatever sort of coulomb interaction you are using) vdw-type = user energygrps = Ca CCA OCA OW HW energygrp_table = Ca OCA Ca CCA OCA OCA OCA OW OCA HW Gromacs is then (at some stage) going to look for a series of files called table.xvg - which is the default 6-12 Lennard Jones that will be used for most of the atoms table_Ca_OCA.xvg - which are the Buckingham interactions between your various atom types. table_Ca_CCA.xvg table_OCA_OCA.xvg table_OCA_OW.xvg table_OCA_HW.xvg These files have the format (and contents) described in section 6.7 of the manual. Finally, you define the various energy groups Ca, OCA and so on in your index.ndx file. The problem is that grompp gives me the following error: atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in different energy groups (incidentally these atoms 1 and 2 are OW and HW) Does this mean that I cannot use different tabulated potentials for different atoms in a molecules? By which I mean that I can't use different tabulated potentials for the OW Ca and HW Ca interactions for example? Final question, as its not clear to me from the manual, if you use a tabulated potential for Lennard Jones and you use mix type 2 (so are you are providing epsilon and sigma in the input rather than A and B) does gromacs still know that it has to manipulate the input parameters in order to get the coefficients of the (tabulated) g(r) and h(r) dispersion and repulsion functions (I mean the g(r) and h(r) defined in section 6.7 of the manual here)? At the same time does it also know not to do anything to the parameters you input for the (tabulated) buckingham potentials (as for a buckingham you are providing A and C)? Many thanks in advance Gareth On Wed, Mar 24, 2010 at 2:25 AM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Matthew Watkins matthew.watk...@ucl.ac.uk Date: Wednesday, March 24, 2010 2:59 Subject: Re: [gmx-users] Using lennard jones and buckingham terms simultaneously To: Discussion list for GROMACS users gmx-users@gromacs.org Hi Gareth, as Vitaly suggested tabulated potentials seem to be the only way to go, it took me a while to get up to speed on the Gromacs way of doing this, so get in touch if you wish. The tables for buck potentials need to include the standard 1/r6 term whilst what would be the 1/r12 term needs to contain exp(- Bx.rho), the C6 and C12 coefficients can then be put in a standard nonbonded section. You'll need a separated table for each pair of interactions that interact with buckingham potential. Each pair must be an energy group as well. If there is a simpler method I'd love to hear it. There's probably not a simpler method because it's not a widely-used procedure. It shouldn't be used at all unless you have established that the combination of functional forms is effective... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Using lennard jones and buckingham terms simultaneously
Hello I would like to use gromacs-4 to do a simulation of a small protein in water and in the presence of calcium carbonate. The potential I have for the calcium carbonate uses Buckingham terms for the interaction between the calcium and carbonate ions, while the protein obviously interacts through Lennard Jones terms. It is my understanding from the manual that it is not possible to mix these two interaction types and so it is not possible to do this simulation. Also when I attempted to mix lennard jones and buckingham terms in a topol.top file grompp complained. Is there anyway around this problem? Many thanks Gareth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
