RE: [gmx-users] AFM pulling rate
Hi, The pull code in Gromacs 3 is pretty messy. The rate is in nm/ps. The force is (unfortunately) not written to the pdo file. You have to redetermine it from the positions, but beware that one of the two groups could jump over the periodic boundary. In Gromacs 4 (and the current CVS) I have completely rewritten the pull code. There are separate xvg output files with only the positions and only the forces. Berk. > Date: Thu, 14 Aug 2008 08:30:35 +0200 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] AFM pulling rate > > Hi, > > The unit of the afm_rate in the GROMACS manual 3.3-1 is nm/ps. > I have read something in an earlier thread on this list that this might > be a typo, it should be nm/timestep. Does anyone know? I would be happy > if I could have that information. > > Moreover, I am a bit confused about the output in the .pdo-file. In the > description of .pdo-files on page 113 in the manual 3.3.-1 it is > written that the .pdo file will contain calculated forces from > AFM-pulling simulation. On the other hand, on page 118, the description > of the AFM output is that it only contains positions of reference group, > pulled group and spring. This is also the only information I can find in > my output. I wonder if there is a way to get the calculated force into > the pdo file or if it should be done manually (force=k*extension)? > > /Malin Bergenstråhle > ___ > 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 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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 pulling rate
Hi, The unit of the afm_rate in the GROMACS manual 3.3-1 is nm/ps. I have read something in an earlier thread on this list that this might be a typo, it should be nm/timestep. Does anyone know? I would be happy if I could have that information. Moreover, I am a bit confused about the output in the .pdo-file. In the description of .pdo-files on page 113 in the manual 3.3.-1 it is written that the .pdo file will contain calculated forces from AFM-pulling simulation. On the other hand, on page 118, the description of the AFM output is that it only contains positions of reference group, pulled group and spring. This is also the only information I can find in my output. I wonder if there is a way to get the calculated force into the pdo file or if it should be done manually (force=k*extension)? /Malin Bergenstråhle ___ 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] AFM Pulling Rate
Hello Bob, have you tried to define the initial position of the AFM-tip? It needs to be set to the position of the COM of the group you want to pull. try and add "afm_init1 = x y z" (x y z = position where the afm should be) to your pull.ppa. Otherwise your afmspring is extended from the beginning so much, that this extension dominates the force on the pulling group and the pullingrate is nearly irrelevant until the system relaxed. ciao Jan > Hello everyone, > I am using AFM pulling to drag a dna base across the surface of a graphene. > I'm > doing this in vaccuum. It seems that the base is pulled at the same rate no > matter what value I specify in afm_rate1. Here is my pull.ppa file: > > runtype = afm > group_1 = ssdna-ions > pulldim = N N Y > afm_rate1 = 0.05 > afm_k1 = 100 > afm_dir1 = 0 0 1 > > I'm using version 3.3. Does anyone know what's going on? > Thanks, > Bob Johnson > > ___ 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] AFM Pulling Rate
Hello everyone, I am using AFM pulling to drag a dna base across the surface of a graphene. I'm doing this in vaccuum. It seems that the base is pulled at the same rate no matter what value I specify in afm_rate1. Here is my pull.ppa file: runtype = afm group_1 = ssdna-ions pulldim = N N Y afm_rate1 = 0.05 afm_k1 = 100 afm_dir1 = 0 0 1 I'm using version 3.3. Does anyone know what's going on? Thanks, Bob Johnson ___ 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
