[gmx-users] 2D simulation of 1 particle in arbitrary analytical potential
Dear all, my colleague would like to calculate free energy profile for a single virtual particle in 2D case given the arbitrary analytical potential defined in x and y positions of the particle. Is it possible to calculate such special simulation in Gromacs? Or how Gromacs should be hacked to be used in such occasion? The reason for use of gromacs is that he would like to use other internal GROMACS routines for free energy calculations. -- Zdraví skoro zdravý Karel Krápník Berka RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz -- 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] Force-field files location and order of reading in Gromacs 4.5.2
Karel Berka wrote: Hi all, I have detected that preference in reading forcefield files in Gromacs 4.5 has probably been changed from Gromacs 4.0.x and older. In older gromacs, when there was forcefield with modification present in my working directory, then it was read preferentially, but now it seems that forcefield is primarily read from /share/top directory - Am I right? The working directory is still searched first. Unfortunately, it is not, otherwise ff in subdirectory of my working directory would have been first one to use for grompp. However, pdb2gmx was working fine for protein and ions around. In 4.5.2 I have tried to have modified gromos53a6.ff in my working directory, but the modification was not used by gromacs. What do you mean not used? Was the wrong force field called when using pdb2gmx? I did not used pdb2gmx since I am simulating membrane protein. The only place when I needed to include forcefield itp was grompp program in use on computer cluster , where I cannot reach /top directory Gromacs prints a list of force field subdirectories in the working directory, then in GMXLIB, and allows you to choose. In the 4.5.x series, you need a full working subdirectory of the modified force field. FF.dat is not used anymore? -Justin -- Zdraví skoro zdravý Karel Krápník Berka RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz -- 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
[gmx-users] Force-field files location and order of reading in Gromacs 4.5.2
Hi all, I have detected that preference in reading forcefield files in Gromacs 4.5 has probably been changed from Gromacs 4.0.x and older. In older gromacs, when there was forcefield with modification present in my working directory, then it was read preferentially, but now it seems that forcefield is primarily read from /share/top directory - Am I right? In 4.5.2 I have tried to have modified gromos53a6.ff in my working directory, but the modification was not used by gromacs. The only way around was to rename the files in any of these manners: 1) directory to gromos53a6b.ff and forcefield.itp therein to have include gromos53a6b.ff/ffnonbonded.itp and gromos53a6b.ff/ffbonded.itp and point md.top to gromos53a6b.ff/forcefield.itp or 2) simply copy all files from ff directory to root and mention them in md.top (forcefield.itp has to be changed afterwards) However both of these modifications are rather messy. -- Zdraví skoro zdravý Karel Krápník Berka RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz -- 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
[gmx-users] Gromacs 4.5-beta2 forcefield troubles
Hi all, I am trying to get 4.5-beta2 running on graphic card but mdrun-gpu (gcc 4.1.3) is still complaining about something in forcefields OPLS - The combination rules of the used force-field do not match the one supported by OpenMM: sigma_ij = (sigma_i + sigma_j)/2, eps_ij = sqrt(eps_i * eps_j). Switch to a force-field that uses these rules in order to simulate this system using OpenMM. Amber03 - OpenMM does not support (some) of the provided interaction type(s) (Improper Dih.) Gromos96 53a6 - OpenMM does not support (some) of the provided interaction type(s) (G96 bonds) Charmm27 - OpenMM does not support (some) of the provided interaction type(s) (Improper Dih.) is there any force field which can be used? -- Zdraví skoro zdravý Karel Krápník Berka RNDr. Karel Berka, Ph.D. Palacký University in Olomouc Faculty of Science Department of Physical Chemistry tř. 17. listopadu 1192/12 771 46 Olomouc tel: +420-585634769 fax: +420-585634769 e-mail: karel.be...@upol.cz -- 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] Invitation to connect on LinkedIn
LinkedIn Karel Berka requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Karel Accept invitation from Karel Berka http://www.linkedin.com/e/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I1933670615_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnPkNdz0TdzcPej59bSpEoQEOdDxjbP0SejcUdj8Vcj4LrCBxbOYWrSlI/EML_comm_afe/ View invitation from Karel Berka http://www.linkedin.com/e/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I1933670615_2/39vdj4Sc3sScPcVckALqnpPbOYWrSlI/svi/ -- Why might connecting with Karel Berka be a good idea? Karel Berka's connections could be useful to you: After accepting Karel Berka's invitation, check Karel Berka's connections to see who else you may know and who you might want an introduction to. Building these connections can create opportunities in the future. -- (c) 2010, LinkedIn Corporation-- 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
