RE: [gmx-users] Pull code, Velocity distribution
Hello, Sorry for bothering you with the same question but just want to make sure that I am getting my results correctly. I run simulations where two blocks of ice are in a sliding contact for 5 ns (using pull code). As an output of the simulation I have pullf.xvg file which I use for 'g_analyze -f pullf.xvg' command and assume that the average force it prints is the average pulling force calculated with the U = 1/2K(vt-(x-x0))^2 harmonic potential. Sorry again for double checking! Cheers, Nino From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Friday, November 02, 2012 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Pull code, Velocity distribution On 11/2/12 10:52 AM, Samadashvili Nino wrote: Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? This should be correct. I am using following parameters: pull = umbrella pull_geometry= direction_periodic pull_dim= Y Y Y pull_start = yes pull_ngroups = 1 pull_group0= ICE_A pull_group1= ICE_B pull_pbcatom0 = 0 pull_pbcatom1 = 0 pull_vec1 = 1 0 0 pull_rate1 = 0.004 pull_k1 = 1 Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B? Yes. Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the distribution plot calculated from the coordinates and they dont match. The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs? How what is calculated? How are you creating your own distributions from the coordinates? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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] Pull code, Velocity distribution
Dear Justin, Thank you for your fast reply. I found out the difference between the plots so no question about the velocity distribution. Cheers, Nino From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Friday, November 02, 2012 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Pull code, Velocity distribution On 11/2/12 10:52 AM, Samadashvili Nino wrote: Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? This should be correct. I am using following parameters: pull = umbrella pull_geometry= direction_periodic pull_dim= Y Y Y pull_start = yes pull_ngroups = 1 pull_group0= ICE_A pull_group1= ICE_B pull_pbcatom0 = 0 pull_pbcatom1 = 0 pull_vec1 = 1 0 0 pull_rate1 = 0.004 pull_k1 = 1 Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B? Yes. Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the distribution plot calculated from the coordinates and they dont match. The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs? How what is calculated? How are you creating your own distributions from the coordinates? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 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] Pull code, Velocity distribution
On 11/2/12 10:52 AM, Samadashvili Nino wrote: Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? This should be correct. I am using following parameters: pull = umbrella pull_geometry= direction_periodic pull_dim= Y Y Y pull_start = yes pull_ngroups = 1 pull_group0= ICE_A pull_group1= ICE_B pull_pbcatom0 = 0 pull_pbcatom1 = 0 pull_vec1 = 1 0 0 pull_rate1 = 0.004 pull_k1 = 1 Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B? Yes. Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the distribution plot calculated from the coordinates and they dont match. The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs? How what is calculated? How are you creating your own distributions from the coordinates? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
