Re: [gmx-users] Is there a way to compile gromacs with MPICH instead of LAM?
Hi, On Saturday, 14. July 2007 01:03, Jim Kress wrote: > Is there a way to compile gromacs with MPICH instead of LAM? I assume fftw > would also have to be recompiled as well. I found an article for gromacs > version 2.xxx but the info in that article did not match anything for > v3.xxx gromacs 3.3.x uses fftw 3.x the parallelisation is implemented in gromacs itself, and not as before in fftw. You can also compile it with mpich ( --enable-mpi and you should have something like /opt/mpich/ch-p4/bin in your path) > > Thanks for your help, > > Jim Kress > > ___ > 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 Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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] problem regarding freezegrps
Hello Users i am carrying out a dimeric protein simulation with G43a1 force field using Gromacs 3.3 I have added some missing residues into my protein using a seperate program. Now before adding water i want to do some simulation in vaccum to minimized those added resideus and also the hydrogens added via pdb2gmx command. For these i am freezing the protein and crystal waters leaving the added residues so that they can freely move. for that i am using the following input (.mdp) file: title = minimizatio in vaccum integrator = steep dt = 0.002 constraints = none nsteps = 500 nstlist = 10 rcoulomb= 1 rvdw= 1 ns_type = simple coulombtype = PME vdwtype = cut-off pbc = no gen_vel = no freezegrps = protein solvent freezedim = Y Y Y Y Y Y emtol = 100.0 emstep = 0.01 With that i have made an index file where i have mentioned two groups with names 'protein' and 'solvent' but inspite of this i am getting the following problem : Fatal error: Group protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. although i have mentioned the index file in the grompp : "aquapo.ndx is the name of index file " grompp -f 1min.mdp -c aquapo_grom.pdb -p aquapo_grom.top -n aquapo.ndx -o 1min.tpr index file used [protein] 1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 26 27 28 29 30 31 32 33 34 35 37 38 39 40 41 42 43 44 45 47 48 49 50 51 52 53 55 56 57 58 59 60 61 64 65 66 67 68 69 70 72 73 74 75 76 77 78 79 80 81 83 85 86 87 88 89 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 110 111 112 113 114 115 116 117 118 119 120 121 122 123 125 126 127 128 129 130 131 132 133 134 136 137 138 139 140 141 142 143 144 146 147 148 149 150 151 152 154 155 156 157 158 159 160 163 164 165 166 167 168 169 171 172 173 174 175 176 177 178 179 180 182 184 185 186 187 188 190 191 192 193 194 195 196 197 198 [solvent] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 please tell what is the reason for this error waiting for your reply With Regards Gurpreet ___ 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] Is there a way to compile gromacs with MPICH instead of LAM?
Is there a way to compile gromacs with MPICH instead of LAM? I assume fftw would also have to be recompiled as well. I found an article for gromacs version 2.xxx but the info in that article did not match anything for v3.xxx Thanks for your help, Jim Kress ___ 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] free energy calculation and constraint distance?
Hello Gromacs users, I am trying to do a free energy calculation, which I have never done before. I have read the manual and the tutorial on the wiki but there is still some issues not clear to me. I am trying to calculate free energy difference of pulling the ligand from a beta-sheet receptor. I understand there is a pull code with different options or it can be done with constraint distances. Please correct me if my procedure is wrong: I want to constraint several distances between the ligand and the receptor and then increase that distance to one where the ligand and receptor are completely separated. For that, I would have to modify my topology where i define [ constraints ] for the distances i want to constrain between the ligand and the receptor and input the bond length for state A(lamda=0) and state B (lamda=1) for each. will the distances defined move the whole ligand away from the receptor? since am only defining several distances between ligand and receptor only. or is it recommended to use the pull code? Any directions is appreciated. Belquis ___ 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] Analytic first derivatives with respect to parameters?
Lee-Ping wrote: Hi there, I'm trying to modify the GROMACS source code to obtain analytic derivatives of the energy and the force with respect to the force field parameters. The goal of this is to help improve force field fitting / optimization routines. Before I begin, has this already been done by anyone? If not, can someone give me a tip on where to actually declare the new variable (say, dE/dk where E is the energy and k is the force constant)? check out: - P. J. van Maaren and D. van der Spoel: Molecular Dynamics Simulations of Water With Novel Shell-Model Potentials J. Phys. Chem. B. 105 pp. 2618-2626 (2001 - David van der Spoel, Paul J. van Maaren and Herman J.C. Berendsen: A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field. J Chem Phys 108 pp. 10220-10230 (1998) in addition there is a bit more along these lines in the program ffscan but not exactly what you are indicating. On the other hand FEP calculations do compute these, for instance changing a force contant from A->B you will get the analytical energy derivative. See manual and relevant references therein. Thanks a lot! - Lee-Ping Wang ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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
[gmx-users] Analytic first derivatives with respect to parameters?
Hi there, I'm trying to modify the GROMACS source code to obtain analytic derivatives of the energy and the force with respect to the force field parameters. The goal of this is to help improve force field fitting / optimization routines. Before I begin, has this already been done by anyone? If not, can someone give me a tip on where to actually declare the new variable (say, dE/dk where E is the energy and k is the force constant)? Thanks a lot! - Lee-Ping Wang ___ 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] which tool to use a measure a user-defined angle in a traj
Hi, Looking through the gmx tools . . . was wondering, which tool would one use (if such a tool exists) to measure the fluctuation of a user-defined angle in a trajectory. For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. How do I define this angle, and which tool would I use to measure it in each frame of my trr? Thanks, Arneh ___ 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] the atomic charges in ligand
Antechamber is a free download. On 7/13/2007 3:25 PM, Rui Li wrote: > Dear Yang Ye, > > Thank you. > I don't have AMBER software.Can I make topology only using Gaussian? > > 在您的来信中曾经提到: > >> From: Yang Ye <[EMAIL PROTECTED]> >> Reply-To: Discussion list for GROMACS users >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] the atomic charges in ligand >> Date:Wed, 11 Jul 2007 17:24:55 +0800 >> >> They use Gaussian primarily. A good example is AMBER, which is >> considered as quite convenient. >> >> http://amber.scripps.edu/antechamber/antechamber.html >> Check its Tutorial and Example section. >> >> After obtaining topology in AMBER format, we use ambconv (available from >> GROMACS' website) to convert to GROMACS' format. >> >> Regards, >> Yang Ye >> >> >> On 7/11/2007 4:55 PM, Rui Li wrote: >> >>> Dear all, >>> >>> In some papers, authors often said that the atomic charges in ligand were >>> > derived > >>> from the electrostatic potential that was determined by QM calculation. Who >>> > can > >>> tell me the detail of this calculation? >>> >>> If I know the atomic charges, Can I use them in my top file? >>> >>> Any reply is appreciated >>> >>> >>> ___ >>> 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 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] the atomic charges in ligand
Dear Yang Ye, Thank you. I don't have AMBER software.Can I make topology only using Gaussian? ÔÚÄúµÄÀ´ÐÅÖÐÔø¾Ìáµ½: >From: Yang Ye <[EMAIL PROTECTED]> >Reply-To: Discussion list for GROMACS users >To: Discussion list for GROMACS users >Subject: Re: [gmx-users] the atomic charges in ligand >Date:Wed, 11 Jul 2007 17:24:55 +0800 > >They use Gaussian primarily. A good example is AMBER, which is > considered as quite convenient. > > http://amber.scripps.edu/antechamber/antechamber.html > Check its Tutorial and Example section. > > After obtaining topology in AMBER format, we use ambconv (available from > GROMACS' website) to convert to GROMACS' format. > > Regards, > Yang Ye > > > On 7/11/2007 4:55 PM, Rui Li wrote: > > Dear all, > > > > In some papers, authors often said that the atomic charges in ligand were derived > > from the electrostatic potential that was determined by QM calculation. Who can > > tell me the detail of this calculation? > > > > If I know the atomic charges, Can I use them in my top file? > > > > Any reply is appreciated > > > > > > ___ > > 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] g_energy doubt
There is a note above selection menu. "enter at a new line or 0" to end your selection. On 7/13/2007 9:12 AM, Mark Abraham wrote: Eduardo Martins Lopes wrote: Greetings all, I have this doubt about using g_energy to extract the box-x and box-y data from the energy.edr. The command i used is g_energy -f MDenergy.edr -ort orienttime.xvg -ora orientave.xvg and when i am prompted to choose wich data i want to retrieve, i type "Box-X Box-Y" and nothing seems to happen, the program keep flashing the prompt as if i havent inserted any data. My question is if i have to type something more (i also tried using comma and tried to retrieve only one data at a time...same problem). Thanks in advance. The code is using scanf (or equivalent), and you need to press enter at least once in order for it to parse the input. 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
