Re: [gmx-users] periodicity in msd calculation
Hi justin, Thanks and sorry for the delayed response. I understand from the link that g_msd choose multiple restarts in a given traj and averages the msd from the restart point to the end of the trajectory. I would like to know if i can avoid such restart points. I would like to choose one starting point as the reference and calculate the msd of each succeeding points with respect to the starting. Thanks Bala On Wed, Aug 22, 2012 at 6:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/22/12 12:12 PM, Bala subramanian wrote: Hi justin, Thanks for the suggestion. I will look at the code. Meanwhile I have one doubt regarding the following option of the g_msd tool. “-trestarttime 10 Time between restarting points in trajectory (ps)” What does this -trestart indicates actually. I did a small trail run on a 100ps trajectory (containing 500 snapshots) with snapshots collected at .2ps interval. In the output file, it is printed as “# MSD gathered over 100 ps with 11 restarts”. Does it mean that the MSD is calculated with 11 different reference coordinates. http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -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 * Only plain text messages are allowed! * 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 -- C. Balasubramanian -- 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] periodicity in msd calculation
On 2/09/2012 1:04 AM, Bala subramanian wrote: Hi justin, Thanks and sorry for the delayed response. I understand from the link that g_msd choose multiple restarts in a given traj and averages the msd from the restart point to the end of the trajectory. I would like to know if i can avoid such restart points. I would like to choose one starting point as the reference and calculate the msd of each succeeding points with respect to the starting. OK, so have a read of g_msd -h and choose what you want to do. Mark Thanks Bala On Wed, Aug 22, 2012 at 6:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/22/12 12:12 PM, Bala subramanian wrote: Hi justin, Thanks for the suggestion. I will look at the code. Meanwhile I have one doubt regarding the following option of the g_msd tool. “-trestarttime 10 Time between restarting points in trajectory (ps)” What does this -trestart indicates actually. I did a small trail run on a 100ps trajectory (containing 500 snapshots) with snapshots collected at .2ps interval. In the output file, it is printed as “# MSD gathered over 100 ps with 11 restarts”. Does it mean that the MSD is calculated with 11 different reference coordinates. http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -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 * Only plain text messages are allowed! * 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
[gmx-users] au virtual site
Dear gromacs users I want to simulate gold nanoparticle by golp force field that needs to determine virtual sites for Au atoms. I read gromacs manual section 5.2.2 and 4.7 but it is not clear that how can I do it and .also I read virtual site tutorial for CO2 but it is for a 3 atomic molecule and I have a crystal by many atoms. I have a pdb file of my nanoparticle contain 600 atoms. How can specify their virtual site? Should I do it by hand? Do you know any command or software that can help me? ramezani -- 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] On creating pdb file using dynamic indices from g_select
Hi everyone! I intend to create a trajectory file (in pdb format) of atoms dynamically indexed by g_select. However, I failed to produce the correct pdb file. Here is how I did it. Kindle help please. 1. I created the index file using g_select for water oxygen atoms within 0.4 nm of Atom 3 g_select -f A.xtc -s A.tpr -select 'resname SOL name OW and within 0.4 of atomnr 3' -on X_ndx. The first few lines of X.ndx look like this [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.000 ] [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.200 ] 685 [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.400 ] 685 1045 2. Then I went into trjconv to create a pdb of these water oxygens trjconv -f A.xtc -s A.tpr -o X.pdb -n X.ndx After keying in Enter, I see a list of the the dynamic groups that looks like the ones above. I have 1 groups in the list corresponding to 1 frames but within each frame having different number/indices of water oxygens. I then get a prompt asking me to select a group. I'm not quite sure what number to type but I tried entering 0, 0 to 1, but both gave me wrong pdb files. They dont match with the indices given in X.ndx. How do I tell Gromacs to create a pdb file for these specific atoms? And next time I use a dynamic index, what do I type Gromacs asks to select a group? Thanks.. Sincerely, Bernard -- 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] On creating pdb file using dynamic indices from g_select
On 2/09/2012 6:03 AM, Mr Bernard Ramos wrote: Hi everyone! I intend to create a trajectory file (in pdb format) of atoms dynamically indexed by g_select. However, I failed to produce the correct pdb file. Here is how I did it. Kindle help please. 1. I created the index file using g_select for water oxygen atoms within 0.4 nm of Atom 3 g_select -f A.xtc -s A.tpr -select 'resname SOL name OW and within 0.4 of atomnr 3' -on X_ndx. The first few lines of X.ndx look like this [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.000 ] [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.200 ] 685 [ resname_SOL_and_name_OW_and_within_0.398_of_atomnr_3_0.400 ] 685 1045 2. Then I went into trjconv to create a pdb of these water oxygens trjconv -f A.xtc -s A.tpr -o X.pdb -n X.ndx After keying in Enter, I see a list of the the dynamic groups that looks like the ones above. I have 1 groups in the list corresponding to 1 frames but within each frame having different number/indices of water oxygens. I then get a prompt asking me to select a group. I'm not quite sure what number to type but I tried entering 0, 0 to 1, but both gave me wrong pdb files. They dont match with the indices given in X.ndx. How do I tell Gromacs to create a pdb file for these specific atoms? And next time I use a dynamic index, what do I type Gromacs asks to select a group? Thanks.. No GROMACS tool can interpret this index file as a dynamic selection, because the tool cannot map the time of a trajectory frame to the selection in the index group. It is a feature expected in GROMACS 5.0, but don't hold your breath. In the meantime, you will have to write a shell script to loop over frames, applying the correct single index group to each frame. trjconv -sep might be a good starting point. Mark -- 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
