[gmx-users] units of eigenvalues of mass-weighted covariance matrix
Dear all, I am confused on the units of the eigenvalues calculated from g_covar of mass-weighted covariance matrix. From the output, it says the unit is (nm\S2\N) but from my understanding, it is supposed to be kg/m2. Thanks for advance for any comments. Regards, Qin ___ 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] Help! A dummy atom definition problem!
Hi Maik, I really did mix up a dummy atom with a virtual site. Any difference? Thank you very much for your help. Regards, Qin On 9/12/07, Maik Goette [EMAIL PROTECTED] wrote: The problem actually is, that you mixed up a dummy atom with a virtual site, I guess. Virtual sites are not allowed to have a mass, as the error message claims. Also, a proper hydrogen should have a mass. If you want a hydrogen to appear, you have to place a particle in A-state which has no non-bonded interaction, i.e. LJ QQ interactions should be zero. If you want to prevent it from flying away, you should put bonded terms to the particle. In the B-state, the QQ and LJ should be there (whereas the LJ interaction for a hydrogen is 0 anyway). 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 opls_999 DUM 0 1.008000 0.000A 0.00 0.00 So, I expect, this is, how it should look like. Be aware of the missing bonded terms in the force field for a DUM particle. Maybe, you want to call it H instead... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top, line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ 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 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 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] Help! A dummy atom definition problem!
Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top, line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ 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] Help! A dummy atom definition problem!
Hi Yang, I was thinking to set mass_B to 0 but what I was supposed to do is converting dummy atoms to H atoms. In my opinion, it wouldn't be H atoms if I set the mass to 0. Am I thinking wrong? Thank you. Regards, Qin On 9/11/07, Yang Ye [EMAIL PROTECTED] wrote: you have set the mass_B to 0 as well. On 9/11/2007 10:54 PM, Wang Qin wrote: Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top, line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ 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 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 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] Help! A dummy atom definition problem!
Thank you so much. On 9/11/07, Yang Ye [EMAIL PROTECTED] wrote: On 9/12/2007 12:39 AM, Wang Qin wrote: Hi Yang, I was thinking to set mass_B to 0 but what I was supposed to do is converting dummy atoms to H atoms. In my opinion, it wouldn't be H atoms if I set the mass to 0. Am I thinking wrong? it's an H as long as it shares the same VDW as H and it carries the same charge as H. Thank you. Regards, Qin On 9/11/07, *Yang Ye* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: you have set the mass_B to 0 as well. On 9/11/2007 10:54 PM, Wang Qin wrote: Hi there, I met the problem when I ran grompp, the errors are: ERROR 1 [file po4lig4tip3.top , line 26741]: virtual site H21 (Res LG4-173) has non-zero mass 1.008 Check your topology. ERROR 2 [file po4lig4tip3.top, line 26741]: virtual site H22 (Res LG4-173) has non-zero mass 1.008 Check your topology. Then I checked my topology file, here were the definition of LG4-173 H21 and H22: ( I want to convert the dummy atoms to H atoms) ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_9991 LG4 H21 21 0. 1.00800 opls_1720.4650 1.00800 22 opls_9991 LG4 H22 22 0. 1.00800 opls_1720.4650 1.00800 in which opls_999 was from what I defined by myself in the force field itp file: opls_999 DUM 0 1.008000 0.000V 0.00 0.00 I changed the both of the mass_A to 0.0, but that didn't help. Does anyone have ideas on that? Thank you very much. Regards, Qin ___ gmx-users mailing list gmx-users@gromacs.org mailto: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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org mailto: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] mailto:[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 ___ 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 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] pressure scaling more than 1%
The system is a protein binding with one ligand and the ligand mutates to another one. The problem is found when lamda=1. First of all I run a energy minimization using an initial structure from the product of lamda=0.9. Then the problem happens when I run a equilibrium. Here is the mdp option: cpp =/usr/bin/cpp integrator = md tinit= 0 dt = 0.002 nsteps = 5 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy= 100 nstxtcout= 5000 xtc-precision= 1000 nstlist = 1 ns_type = grid Pcoupl = berendsen tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 tcoupl = nose-hoover tc_grps = system tau_t= 0.1 ref_t= 300 constraints = none constraint-algorithm = lincs shake-tol= 0.0001 lincs-order = 12 lincs-warnangle = 30 coulombtype = pme rcoulomb = 1.0 epsilon-r= 1 vdw-type = switch rvdw-switch = 1.0 rvdw = 1.3 DispCorr = EnerPres fourierspacing = 0.08 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 6 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = yes free_energy = yes init_lambda = 1.0 delta_lambda = 0 sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 Thanks. On 8/8/07, Mark Abraham [EMAIL PROTECTED] wrote: Wang Qin wrote: Dear all, I am trying to do a FEP. In the equilibrium step, it fails after about 500 steps with a warnning: pressure scaling more than 1%, mu: 1.06718 1.06718 1.06718. I searched the old discussion about it and then try to increase the tau_p to 2 till 10. But it just goes futher but still meets the problem at the end. Any idea about it? Not unless you tell us how you prepared this system. Almost certainly the initial structure is too far from the constant-P equilibrium state. Follow the kind of things that the tutorial material does, and also check out this link http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation 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 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] dummy atom definition prob in FEP
Thank you, Maik. I do want to do standard FEP and thank you for telling me that FEP don't go with virtual sites. It does help. BTW, may I ask you why I should define a none_zero mass for a dummy atom? Thanks, Qin On 8/8/07, Maik Goette [EMAIL PROTECTED] wrote: Friend... What are you trying to do??? If you want to do standard FEP with growing something into dummy (NOT virtual site) or from dummy, you must not use virtual sites! Virtual sites in fact, have no mass; neither in A- nor in B-state. Please read the fManual about virtual particles, their usage and why they exist in GROMACS (hint, delocalized charge) As far as I know, you can't morph a virtual site to a real particle. I also think, It wouldn't make much sense, though. If you want to morph away e.g. a proton, define a dummy in the b-state, which has no LJ parameters (eps and sigma=0) and no charge, but still the original mass. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Wang Qin wrote: Hi, Thanks for reply. It seems that specifying mass_B = mass_A doesn't help to solve the problem. However, if I don't use the directory [virtual_site#] the errors disappear! What's the result if I do this? Is the directory necessary in the FEP calculation to define the dummy atoms? Thanks, Qin On 7/20/07, *Stéphane Téletchéa* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Wang Qin a écrit : Hi there, I have a problems when I do a FEP calculation. Below is how I defined dummy atoms in the topology file: [atom] ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_1721 LG6 H21 21 0.4650 1.00800 opls_0 0. 0.00 22 opls_1721 LG6 H22 22 0.4650 1.00800 opls_0 0. 0.00 .. I think you need to specify the mass_B=mass_A, at least this is how it is setup in the tutorials i've done (the one from Berk Hess and the other one from David Mobley). I've also done calculations without setting the mass for B (like you did) and did not encounter any problem, the error you're seing could thus come from another part of your system. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search 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] mailto:[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 ___ 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 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] pressure scaling more than 1%
Dear all, I am trying to do a FEP. In the equilibrium step, it fails after about 500 steps with a warnning: pressure scaling more than 1%, mu: 1.06718 1.06718 1.06718. I searched the old discussion about it and then try to increase the tau_p to 2 till 10. But it just goes futher but still meets the problem at the end. Any idea about it? Regards, Qin ___ 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] dummy atom definition in FEP
Hi everyone, I am just thinking about if in FEP calculation, I have given the position information for dummy atoms in the directory of [atoms], do I need to give the directory [virtual_sites] as well? Since I met a problem when I was giving the [virtual_sites] directory and the problem went away when I deleted it, I want to make sure if what I did is right. Here is the informaiton from my topology file: [atoms ] ;nr typeresnr residue atomcgnrcharge mass type_B charge_Bmass_B 21 opls_172 1 LG6 H21 210.4650 1.00800 opls_9990. 1.00800 22 opls_172 1 LG6 H22 220.4650 1.00800 opls_9990. 1.00800 ;opls_999 is defined by myself with an atomtype V and 0 charge 0 mass then is this directory necessary? [virtual_sites3] ;Site from from from funct theta d 21 10 2 1 3 108 0.109 22 11 4 3 3 108 0.109 I am quite confused. Please help. Regards, Qin ___ 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] dummy atom definition prob in FEP
Hi, Thanks for reply. It seems that specifying mass_B = mass_A doesn't help to solve the problem. However, if I don't use the directory [virtual_site#] the errors disappear! What's the result if I do this? Is the directory necessary in the FEP calculation to define the dummy atoms? Thanks, Qin On 7/20/07, Stéphane Téletchéa [EMAIL PROTECTED] wrote: Wang Qin a écrit : Hi there, I have a problems when I do a FEP calculation. Below is how I defined dummy atoms in the topology file: [atom] ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_1721 LG6 H21 21 0.4650 1.00800 opls_0 0. 0.00 22 opls_1721 LG6 H22 22 0.4650 1.00800 opls_0 0. 0.00 .. I think you need to specify the mass_B=mass_A, at least this is how it is setup in the tutorials i've done (the one from Berk Hess and the other one from David Mobley). I've also done calculations without setting the mass for B (like you did) and did not encounter any problem, the error you're seing could thus come from another part of your system. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ 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 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] dummy atom definition prob in FEP
Hi there, I have a problems when I do a FEP calculation. Below is how I defined dummy atoms in the topology file: [atom] ;nr typeresnr residue atomcgnrcharge masstype_B charge_Bmass_B 21 opls_1721 LG6 H21 21 0.4650 1.00800 opls_0 0. 0.00 22 opls_1721 LG6 H22 22 0.4650 1.00800 opls_0 0. 0.00 .. [virtual_sites3] ;Site from from from funct theta d 21 10 2 1 3 108 0.09450 22 11 4 3 3 108 0.09450 [bonds] ... The problem is when I ran grompp, there are 2 fatal errors, saying: ERROR 1: virtual site H21 (Res LG6-173) has non-zero mass 1.008 Check your topology. ERROR 2: virtual site H22 (Res LG6-173) has non-zero mass 1.008 Check your topology. --- Program grompp_mpi, VERSION 3.3.1 Source code file: grompp.c, line: 1180 Fatal error: There were 2 errors in input file(s) --- Does anyone know anything about it? Is there any mistake I made? How should I do? Thank you very much. Regards, Qin ___ 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
