[gmx-users] FEP source code
Hello GMX-people I am trying to locate the source code files regarding free energy perturbation (FEP) calculations. Does anyone have an idea? regards, -- Murat Cetinkaya, PhD Max-Planck-Institute for Metals Research Protein Mechanics and Evolution Group Bioquant BQ0031, Universitaet Heidelberg INF 267, 69120 Heidelberg, Germany Tel +49 6221-54-51268 Fax +49 6221-54-51483 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] OPLS-AA dihedral angles
Hi all, I am trying to obtain proper dihedral parameters for CA-CT-CT-CA type, which is not in the OPLS-AA database. I have found a set for periodic dihedral type (from AMBER database) but I dont know how to convert that into RB form. GMX Manual does not mention how to convert periodic proper terms into RB form. So, my questions are:1) Can I put periodic dihedral parameters into OPLS-AA database?2) If (1) is no, then how can I convert periodic type into RB form? Is there any specific point to consider when using AMBER terms? (e.g. multiplying coefficients by 2) 3) Does anyone readily have the CA-CT-CT-CA dihedral parameters :) Thanks in advance,Murat CETINKAYA The Pennsylvania State University ___ 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] AFM pull and ensembles
Hi all,I have two questions about PMF calculations. 1) Which one is more suggested for an AFM pull simulation, an NVT or an NPT ensemble? I am trying both vacuo and solvated runs (with OPLS-AA ff). 2) My second question is about solvation: I found out that pulling action is much smoother in solvent than in vacuo. It may be bad to have energy and rms jumps in vacuo. On the other hand, I think it would be better for estimating forces and energy differences with an abrupt change in the system. What is you opinion about effects of solvation?Thanks in advanceMurat Cetinkaya___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] RE: pdb2gmx error
I will do what you suggest David. But, I have plenty of these lines, so I was avoiding that method. However, it seems the only solution right now. Thanks Murat > Hi all, > > I have a small problem with pdb2gmx. I have a non-standard residue with rtp > parameters entered manually into oplsaa database. When I try to convert my pdb > file into gro, I get: > - > Program pdb2gmx, VERSION 3.3.1 > Source code file: toputil.c, line: 94 > > Fatal error: > Increase MAXSLEN in src/kernel/grompp.h to at least 35, or shorten your > definition of bonds like 2.87441 0.58158 2.092 -5.54799 0 0 to at most 31 put a string there, say "my_rb_dih_1", and then add the real definition in the ffoplsaabon.itp file. > - > Mentioned line is one of my RB dihedral parameters. > > I got the same problem with gromacs 3.2.1, but I dont know how I got rid of it. > I also could not find grompp.h in the mentioned location. > > I cannot truncate my parameters in order to fit for 31 character-space, so I am > clueless. > -- David. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] pdb2gmx error
Hi all, I have a small problem with pdb2gmx. I have a non-standard residue with rtp parameters entered manually into oplsaa database. When I try to convert my pdb file into gro, I get: - Program pdb2gmx, VERSION 3.3.1 Source code file: toputil.c, line: 94 Fatal error: Increase MAXSLEN in src/kernel/grompp.h to at least 35, or shorten your definition of bonds like 2.87441 0.58158 2.092 -5.54799 0 0 to at most 31 - Mentioned line is one of my RB dihedral parameters. I got the same problem with gromacs 3.2.1, but I dont know how I got rid of it. I also could not find grompp.h in the mentioned location. I cannot truncate my parameters in order to fit for 31 character-space, so I am clueless. I will appreciate any help. Thanks in advance. Murat Cetinkaya ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] isomerization with RB diheadrals
Hello gmx users, I am trying to induce an isomerization by changing two RB-dihedrals. However, I could not figure out how to do it by changing the available parameters. I suppose it should be some +/- modification with the same magnitudes. Nevertheless, I could not find any documentation about it. Any advice is greatly appreciated. quick question: Do I (also) have to modify the improper dihedrals in order to satisfy planarity? Thanks Murat Cetinkaya ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] free energy questions
Hi, I have a couple of questions about FE calculations. I am following the tutorial by Dill group for calculating the solvation FE of a non-standard residue. 1) Trivial questions first: It is advised to use PME with opls, is it possible to use PME in vacuo? As far as I know PME depends on periodicity, which is shut-off in vacuo. 2) Should I extract dv/dl values from my .edr file to get dG? Can I use dgdl.xvg file? It is trivial but I am confused about this procedure. 3) I have smooth simulations when init_lambda < 1. But When I get to lambda =1, I sometimes get enormously high energy values (in a fluctuating manner) for my system. What could be the problem? 4) As you see in the mdp file, I used sc_alpha = 0. Otherwise, my system gives out error. Is it bad to use sc_alpha =0? 5) Should I use FE parameters in my energy minimization simulations? Normally, I used my minimized lambda=0 structure as input for other lambda simulations without doing further EM. I also tried to include lambda values in my EM files and I got junk results (.gro files and energy values). and this is my mdp file for in vacuo MD: title= MD in vacuo cpp = /lib/cpp include = -I/../EM/ integrator = sd tinit= 0 dt = 0.001 nsteps = 250 ; number of steps for center of mass motion removal = nstcomm = 100 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 5000 nstxtcout= 0 xtc-precision= 1000 ;xtc_grps = Protein nstlist = 10 ns_type = grid ;pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb = 1.2 rcoulomb_switch = 1.0 epsilon-r= 1.0 vdw-type = Shift rvdw = 1.2 rvdw_switch = 1.0 DispCorr = EnerPres ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 1.0 ref_t= 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = No tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = yes init_lambda = 1.0 delta_lambda = 0 sc_alpha =0.0 ;sc-power =1.0 sc-sigma = 0.3 ; GENERATE VELOCITIES FOR STARTUP RUN = meaningful only with md integrator gen_vel = yes gen_temp = 300 gen_seed = -1 thanks in advance. Murat CETINKAYA, M.Sc. BioNanoMaterials Group, Dept. of Engr. Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 office: (814) 863 9967 web: www.personal.psu.edu/muc176 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] free energy and fatal error
> Message: 1 > Date: Mon, 26 Jun 2006 12:12:49 +0200 > From: Maik Goette <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] free energy and fatal error > To: Discussion list for GROMACS users I am using GROMACS 3.2.1. > > Hi > > Are those atoms mentioned, perturbed ones? Yes, all atoms are perturbed. > I think, it has nothing to do with the error, you experience, but > delta_lambda should be 1/number of steps, if you want to do TI from 0 to 1. I follow the solvation FE tutorial by Dill group. These are the parameters that they provide > Anyway, maybe you should look at the energies on these atoms and perhaps > recheck your bonded parameters... dgdl file shows an increase like this (for init and delta lambda =0): 0 58.799 0.001 -3923.71 0.002 -5081.52 0.003 -4004.63 0.004 -4382.1 0.005 -6933.78 0.006 -7533.55 0.007 -158.663 0.008 -7881.4 0.009 -776183 0.01 nan 0.011 nan 0.012 nan 0.013 nan 0.014 nan 0.015 nan 0.016 nan 0.017 nan 0.018 nan 0.019 nan > More details, like your mdp-file, would be helpful. Here is the full input file: title= NVT_EQ in vacuo cpp = /lib/cpp include = -I/../EM/ integrator = sd tinit= 0 dt = 0.001 nsteps = 1 nstcomm = 100 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy= 100 nstxtcout= 1000 xtc_precision= 1000 xtc_grps = Protein energygrps = Protein nstlist = 10 ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 10 ;0.1 in tutorial, but this may be better ref_t= 300 ;pbc = xyz rlist= 1.4 coulombtype = Shift rcoulomb = 1.2 rcoulomb_switch = 1.0 epsilon_r= 1.0 vdwtype = Shift rvdw = 1.2 rvdw_switch = 1.0 constraints = none ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 > > 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/ > > > MURAT CETINKAYA wrote: > > Hi, > > > > I am trying to calculate solvation free energy of a non-standard residue and I > > have problems in vacuum runs. > > > > I defined a dummy atom for every single atom in the molecule (0 charge and > > non-bonded parameters) and I input every single bonded interaction values > > manually (in order to prevent any errors resulting from that). > > > > I minimized my molecule with l-bfgs and steep. If do free energy = no, I can do > > my NVT run in vacuo without any problems. However, when I set: > > > > free_energy = yes > > init_lambda = 0.0 > > delta_lambda = 0 > > sc_alpha = 0.5 > > sc-power = 1.0 > > sc-sigma = 0.3 > > > > I get the following error: > > step 0Warning: 1-4 interaction between 21 and 23 at distance larger than 2.4 nm > > These are ignored for the rest of the simulation > > turn on -debug for more information > > Fatal error: ci = -2147483648 should be in 0 .. 63 [FILE nsgrid.c, LINE 218] > > > > As I said, every bonded interaction value is entered manually (A = B values) and > > structure seems minimized. > > > > Any ideas appreciated > > thanks > > Murat CETINKAYA, M.Sc. > > BioNanoMaterials Group, > > Dept. of Engr. Science and Mechanics, > > The Pennsylvania State University, > > University Park, PA 16802 > > office: (814) 863 9967 > > web: www.personal.psu.edu/muc176 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] free energy and fatal error
Hi, I am trying to calculate solvation free energy of a non-standard residue and I have problems in vacuum runs. I defined a dummy atom for every single atom in the molecule (0 charge and non-bonded parameters) and I input every single bonded interaction values manually (in order to prevent any errors resulting from that). I minimized my molecule with l-bfgs and steep. If do free energy = no, I can do my NVT run in vacuo without any problems. However, when I set: free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 I get the following error: step 0Warning: 1-4 interaction between 21 and 23 at distance larger than 2.4 nm These are ignored for the rest of the simulation turn on -debug for more information Fatal error: ci = -2147483648 should be in 0 .. 63 [FILE nsgrid.c, LINE 218] As I said, every bonded interaction value is entered manually (A = B values) and structure seems minimized. Any ideas appreciated thanks Murat CETINKAYA, M.Sc. BioNanoMaterials Group, Dept. of Engr. Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 office: (814) 863 9967 web: www.personal.psu.edu/muc176 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] oplsaa and lincs error
Hi gmx users, I am trying to perform Free Energy calculations on a non-standard residue using oplsaa force field. Two problems arise: 1) When I try to minimize in vacuo, atoms split apart and molecule is destroyed. This is independent of the algorithm. I tried with and witohut constraints on the system. This is the input file for in vacuo: title= EM in vacuo cpp = /lib/cpp include = -I/./ integrator = steep nbfgscorr= 50 nstcgteep= 1 nsteps = 5000 emtol= 1 niter= 20 nstxout = 10 nstvout = 0 nstfout = 0 nstlog = 10 nstenergy= 10 nstxtcout= 0 xtc-precision= 100 xtc_grps = Protein energygrps = Protein nstlist = 1 ns_type = grid ;pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb = 1.0 epsilon_r= 1.0 vdw-type = Cut-off rvdw = 1.0 constraints = all-bonds ; EWALD/PME/PPPM parameters pme_order= 12 ewald_rtol = 1e-05 optimize_fft = yes fourierspacing = 0.15 2)If I solvate the system with tip4p, I can do minimization (although ending very early) and I can perform POSRE NVT equilibration. When I switch to NVT w/o restrains on the peptide, system gives out LINCS errors (relative constraint deviation) although I dont use any constraints. I also turned off PME. I saw some emails talking about tip4p constraints. But I am clueless about in vacuo. any help appreciated. Murat CETINKAYA, M.Sc. BioNanoMaterials Group, Dept. of Engr. Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 office: (814) 863 9967 web: www.personal.psu.edu/muc176 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] oplsaa force field and dummy atoms
Yes, I did a detailed search about it. The confusing part is nobody complained about using dummy atoms. Am I missing something? thanks. From: "David Mobley" <[EMAIL PROTECTED]> I think I've seen this one in the archives before. Did you try searching the list? On 6/19/06, MURAT CETINKAYA <[EMAIL PROTECTED]> wrote: > Hi GMX users, > > My question is to calculate solvation free energy of a non-standard residue (I > managed to define it into oplsaa database). I followed the tutorial prepared by > groningen group (http://md.chem.rug.nl/education/Free-Energy_Course/index.html) > > My problem is how to use dummy atoms in ffoplsaa for my calculations. I think > DUM is for tip4p water and there are other types like MNH3 and MCH3A. Question: > > Can I use the already defined dummy atoms (MNH3 etc) for my system? I dont think > that these will be enough for my special molecule. Or, should I define new > dummy atoms having same bonded interaction parameters (which should have the > same procedure like defining the molecule originally). I hope my question is > clear enough :) > > Thanks in advance Murat CETINKAYA, M.Sc. BioNanoMaterials Group, Dept. of Engr. Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 office: (814) 863 9967 web: www.personal.psu.edu/muc176 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] oplsaa force field and dummy atoms
Hi GMX users, My question is to calculate solvation free energy of a non-standard residue (I managed to define it into oplsaa database). I followed the tutorial prepared by groningen group (http://md.chem.rug.nl/education/Free-Energy_Course/index.html) My problem is how to use dummy atoms in ffoplsaa for my calculations. I think DUM is for tip4p water and there are other types like MNH3 and MCH3A. Question: Can I use the already defined dummy atoms (MNH3 etc) for my system? I dont think that these will be enough for my special molecule. Or, should I define new dummy atoms having same bonded interaction parameters (which should have the same procedure like defining the molecule originally). I hope my question is clear enough :) Thanks in advance Murat CETINKAYA, M.Sc. BioNanoMaterials Group, Dept. of Engr. Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 office: (814) 863 9967 web: www.personal.psu.edu/muc176 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] cis-trans isomerization in Ryckaert Bellemans dihedrals
Hi all, I am trying to perform FEP on a double ring structure such that I want to see cis-trans isomerization of the molecule by shifting the reference angle by 180 degrees. How can I apply this shift on RB parameters of my dihedral? I read the manual, but transformation of parameters into RB form is not clear enough for me. thanks in advance. Murat CETINKAYA, M.Sc. BioNanoMaterials Group, Dept. of Engr. Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 office: (814) 863 9967 web: www.personal.psu.edu/muc176 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
