Re: [gmx-users] acetone parameter
Mark Abraham wrote: JMandumpal wrote: Dear list, I would like to simulate aqueous acetone system using UA OPLS potentials. I chose the following atoms types, given below (TABLE ONE), for acetone, with united atom for Methyl groups. TABLE ONE -- [ atoms ] ; nrtyperesnr resid atom cgnr chargemass 1opls_0691 ACETCAA10.000 15.0350 2opls_2801 ACETC_210.470 12.0110 3opls_0691 ACETCAD10.000 15.0350 4opls_2811 ACETO_21 -0.470 15.9994 --- But on the other hand, when I checked the literature, JPC 94, 1990, p.1683, I found out, the parameters are given in the following manner, TABLE TWO : TABLE TWO atom types charge sigma epsilon CH3 0.062 3.910 0.160 C0.300 3.750 0.105 O -0.424 2.960 0.210 ** For keeping total charge in the system to zero, I used the opls_069 for methyl group (zero charge), in my input file, compared to what has been published. I would like to know whether the parameters (charge) I chose is right, else which atom type I must use for methyl group. Different models will have different charges. What is correct to use depends on how those models were parameterized to interact with which other force fields, and for what purpose they were intended. Finding this out and making these decisions is your job, not ours. Apart from that: just test it. Simulate bulk acetone and compare the properties to experimental data (densite DHvap etc.) -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dielectric constant
Mark Abraham wrote: [EMAIL PROTECTED] wrote: Hello, I'm interested in running a simulation in which the box will be divided in to two different dielectric constants separated at a plane. Is it possible to do that in Gromacs? Possible, yes. However it is not implemented, and it is not a trivial change to do so. If you do that (and implement a position dependent epsilon_r that is not 1) your system will most likely explode. Using epsilon_r different from 1 means that the weighting between Coulomb and Van der Waals forces will be different. For e.g. water e_r 1 will make the system explode, e_r 1 will make it implode. Your choice. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Concatenate TPR files after restart
There is no need to concatenate .tpr files; they contain structure and parameter information, and thus is does not make sense to add them together. To analyze the whole trajectory, supply g_hbond the starting .tpr file along with your trajectory file. -Justin -- Ok Justin, I didn't know that the tpr files contain only structure and parameter information. That really wouldn't make sense to merge both. Well, thanks! -- ___ Ricardo Oliveira dos Santos Soares Post-graduation Student in Biological Physics University of Sao Paulo - USP Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP Phone: 55 (16) 3602-4840 Curriculum Lattes - http://lattes.cnpq.br/0777038258459931 ___ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Conformation search!
Dear Anthony, You can apply distance restraints to pairs of atoms, e.g. CA atoms in your domains. Check the manual. Ran. Anthony Cruz wrote: On Thursday 17 April 2008 9:13 pm, Mark Abraham wrote: Anthony Cruz wrote: Hi User: We have a protein with two domains. This two domains were connected by two linkers of different length. We want to study the different conformation that the protein domains can adopt depending the length of the linkers without loosing the secondary structure feature present. I was thinking in use some position restrain in the backbone atoms of the domains and leave the linkers and all the side chains to move freely but this aproach will not let the system to change the conformation. I'm using GROMACS 3.2.1. With a dihedral constraint it will be posible to what I want to do? How can I do it? There is any other option to do this? This didn't get an answer earlier this week, probably because of the way you've worded it. It's a bad idea to presuppose things about the solution in your description, because if you're right then people wonder why you are being lazy and not trying it out, and if you're wrong then you're distracting people from identifying the real solution... see http://catb.org/~esr/faqs/smart-questions.html#symptoms You seem to want to let your domains move relative to each other, but also to deny them much internal freedom. So what you want to do is enforce (some of) their internal structure. Thus, use distance restraints. Mark Thank you for your answer. But probably I don't make my point clear. I have a protein with two units (domains). I think that distant restraint will restraint the distance between the two domains or units... This is done by the linkers between them. I want them to move freely but not to change its structure, like freezing the backbone and let the rest to move freely. How I could do this? I think that I explain my problem better this time. I presuppose things about the solution because I don't want that the people in the mailing list think that I just have the problem and not try to resolve it my self. Thank you for your advise Mark I will try to change the way I make the questions. Anthony ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Conformation search!
Anthony Cruz wrote: You seem to want to let your domains move relative to each other, but also to deny them much internal freedom. So what you want to do is enforce (some of) their internal structure. Thus, use distance restraints. Mark Thank you for your answer. But probably I don't make my point clear. I have a protein with two units (domains). I think that distant restraint will restraint the distance between the two domains or units... This is done by the linkers between them. I want them to move freely but not to change its structure, like freezing the backbone and let the rest to move freely. How I could do this? Distance restraints to enforce their *internal structure*... So don't restrain all the distances, just some cunningly chosen ones inside each domain. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv error
Ragothaman Yennamalli wrote: I wanted to truncate a trajectory file and when I use trjconv tool, I get an error: Fatal error: /media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc is not a trj file, exiting The file is able to read by gmxcheck... What could be the problem? What GROMACS version? What OS? Have you tried copying the file elsewhere and reading from there? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] residual negative charge?
Hello everybody, I'm trying to use gromacs to model an aza-type macrocycle (17 atoms around the ring). The structure does not include any aminoacids or sugars so, I'm building the itp file by hand. I started with a base topology from the PRODRG server and then added all the missing hydrogens (I want to use OPLS/AA). The problem is that, after assigning all the atom types as best as I could, I end up with a residual charge = -0.034. The macrocycle itself should be neutral. Does this mean I need to develop new parameters? Is there any way to fix this without reparametrizing? Thanx Victor M. Rosas García Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] residual negative charge?
Hi Victor, Assigning the right parameters for a molecule is a difficult task, and a single run of PRODRG is usually just the beginning. Search the archives and maybe also the wiki for more information, and read a few papers where simulations of proteins were done with hetero-molecule if you haven't done so already. It's not a good idea to have a residual charge. You can obviously scale this, but I would start by verifying that the PRODRG charges make sense in any case. Ran Victor Manuel Rosas-Garcia wrote: Hello everybody, I'm trying to use gromacs to model an aza-type macrocycle (17 atoms around the ring). The structure does not include any aminoacids or sugars so, I'm building the itp file by hand. I started with a base topology from the PRODRG server and then added all the missing hydrogens (I want to use OPLS/AA). The problem is that, after assigning all the atom types as best as I could, I end up with a residual charge = -0.034. The macrocycle itself should be neutral. Does this mean I need to develop new parameters? Is there any way to fix this without reparametrizing? Thanx Victor M. Rosas García Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Water in graphite plates
Dear All, I want to model water transport sandwitched within two graphite surfaces. Do you know how to generate the structure file of graphite surface? Thank you very much! Hero Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] water can't freeze
Hi gmx users, I'm a new Gromacs user. Till now, I can get pretty good simulation of ice melting to water, but why can't I simulate water freezing to ice? The .top and .gro files used for water freezing simulation are generated by ice melting to 310K. I changed the temperature in .mdp file to 230K, but after mdrun, the water was still water, it can't freeze? How can I get water freezing to ice? I paste mdp for your reference. Thanks. best, xiupeng title= icing at 230 K with cuffoff cpp = /lib/cpp integrator = md ;Time step dt = 0.002 nsteps = 10 ;Output control nstxout = 10 nstvout = 10 nstlog = 100 nstenergy= 100 nstxtcout= 100 ;Neigbour searching nstlist = 10 ns_type = grid rlist= 0.8 ;Non bonded interaction coulombtype = pme optimize_fft = yes fourierspacing = 0.2 pme-order= 6 ewald-rtol = 1e-05 rcoulomb = 0.8 vdw-type = Cut-off rvdw = 0.8 DispCorr = EnerPres ;Temperature coupling tcoupl = berendsen tc-grps = System tau_t= 0.1 ref_t= 230 ;Pressure coupling pcoupl = berendsen pcoupltype = isotropic tau_p= 1.0 compressibility = 5e-5 ref_p= 1.0 gen_temp = 230.0 constraints = all-bonds ; generate velocities gen_vel = yes gen_seed = 173529 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
