[gmx-users] glibc detected *** g_sas_d
Hello all, I'm trying to know how the surface area of a nano-drop changes during the evaporation in the vacuum. When I filter the trajectory of non-evaporated molecules by trjconv and use g_sas for calculation of their surface, it usually crash (I'm using version of 4.5.5). Is there still this issue in the 4.6.*? How it can be resolved? Best Rasoul -- 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] glibc detected *** g_sas_d
Bellow are commands and error message: 1- trjconv_d -f traj.xtc -n maxclust.ndx -o traj_out.xtc 2-g_sas_d -f traj_out.xtc -n maxclust.ndx -o surface.xvg -nopbc glibc detected *** g_sas_d: malloc(): memory corruption: 0x016dfcd0 Rasoul On Thu, Jul 18, 2013 at 1:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/13 6:52 AM, Rasoul Nasiri wrote: Hello all, I'm trying to know how the surface area of a nano-drop changes during the evaporation in the vacuum. When I filter the trajectory of non-evaporated molecules by trjconv and use g_sas for calculation of their surface, it usually crash (I'm using version of 4.5.5). What's the error message? What's your command? Is there still this issue in the 4.6.*? How it can be resolved? Have you tried version 4.6? That's the quickest way to know. If there are still problems, you'll need to provide more information. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] glibc detected *** g_sas_d
Justin, I just ran this calculations on VERSION 4.6-GPU-dev-20120501-ec56c and I will let you know about the outcomes. Rasoul On Thu, Jul 18, 2013 at 1:09 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Bellow are commands and error message: 1- trjconv_d -f traj.xtc -n maxclust.ndx -o traj_out.xtc 2-g_sas_d -f traj_out.xtc -n maxclust.ndx -o surface.xvg -nopbc glibc detected *** g_sas_d: malloc(): memory corruption: 0x016dfcd0 Rasoul On Thu, Jul 18, 2013 at 1:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/13 6:52 AM, Rasoul Nasiri wrote: Hello all, I'm trying to know how the surface area of a nano-drop changes during the evaporation in the vacuum. When I filter the trajectory of non-evaporated molecules by trjconv and use g_sas for calculation of their surface, it usually crash (I'm using version of 4.5.5). What's the error message? What's your command? Is there still this issue in the 4.6.*? How it can be resolved? Have you tried version 4.6? That's the quickest way to know. If there are still problems, you'll need to provide more information. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] glibc detected *** g_sas_d
/4.6.0-phase3/lib/libgmxana_d.so.6 7f3b99203000-7f3b99402000 ---p 00245000 00:19 2309614127 /nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmxana_d.so.6 7f3b99402000-7f3b99403000 r--p 00244000 00:19 2309614127 /nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmxana_d.so.6 7f3b99403000-7f3b9940c000 rw-p 00245000 00:19 2309614127 /nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmxana_d.so.6 7f3b9940c000-7f3b9940d000 rw-p 00:00 0 7f3b9940d000-7f3b9942c000 r-xp 00:0f 2285702 /lib64/ld-2.11.1.so 7f3b995f7000-7f3b995fd000 rw-p 00:00 0 7f3b99602000-7f3b9962b000 rw-p 00:00 0 7f3b9962b000-7f3b9962c000 r--p 0001e000 00:0f 2285702 /lib64/ld-2.11.1.so 7f3b9962c000-7f3b9962d000 rw-p 0001f000 00:0f 2285702 /lib64/ld-2.11.1.so 7f3b9962d000-7f3b9962e000 rw-p 00:00 0 7fff97796000-7fff977aa000 rwxp 00:00 0 [stack] 7fff977aa000-7fff977ae000 rw-p 00:00 0 7fff977ff000-7fff9780 r-xp 00:00 0 [ vdso] ff60-ff601000 r-xp 00:00 0 [ vsyscall]Aborted --- If you still think that results of 4.6.3 might be necessary, I will do it. Rasoul On Thu, Jul 18, 2013 at 2:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/13 8:04 AM, Rasoul Nasiri wrote: Justin, I just ran this calculations on VERSION 4.6-GPU-dev-20120501-ec56c and I will let you know about the outcomes. The outcome of 4.6.3 would be more interesting than an outdated development version. -Justin Rasoul On Thu, Jul 18, 2013 at 1:09 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Bellow are commands and error message: 1- trjconv_d -f traj.xtc -n maxclust.ndx -o traj_out.xtc 2-g_sas_d -f traj_out.xtc -n maxclust.ndx -o surface.xvg -nopbc glibc detected *** g_sas_d: malloc(): memory corruption: 0x016dfcd0 Rasoul On Thu, Jul 18, 2013 at 1:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/13 6:52 AM, Rasoul Nasiri wrote: Hello all, I'm trying to know how the surface area of a nano-drop changes during the evaporation in the vacuum. When I filter the trajectory of non-evaporated molecules by trjconv and use g_sas for calculation of their surface, it usually crash (I'm using version of 4.5.5). What's the error message? What's your command? Is there still this issue in the 4.6.*? How it can be resolved? Have you tried version 4.6? That's the quickest way to know. If there are still problems, you'll need to provide more information. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http
[gmx-users] Maxwell-Stefan diffusion coefficient
Hello all, Is it possible one can calculate molecular diffusion of multi-component systems in the gas phase by GROMACS? This quantity is very important in evaporation of fluids when liquid and vapour phases are in quasi-equilibrium state. Any help would be highly appreciated? Best Rasoul -- 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] Reduced Units
Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- 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] Reduced Units
Are you sure lattice cell set up in f.c.c structure has been explained there for the positions of molecules? On Thu, May 16, 2013 at 3:28 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Does manual 2.3 help? On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- 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 -- 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] Periodic Boundary Condition in evaporation of droplets
Dear All, I just had a question regarding using the PBC for evaporation of clusters. Due to PBC the evaporated molecules again come back to drop (re-condensation). For me such a process is physically meaning less. Shall I ask a question from GMX users about this issue. How we can eliminated this unphysical process? Please ote that I'm not interest to use vacuum since vapour pressure of nanodrop is essential foR my MD simulation. Many thanks Rasoul -- 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] Periodic Boundary Condition in evaporation of droplets
Dear Richard, Thanks for your reply and comments. To be honest, I have read the couple of papers about the evaporation of droplets using PBC. There are controversial discussions on this question how to evaluate size of box so that PBC issue can be eliminated. While some author believe that size of box should be at least 10 times larger than diameter of drop, others think that this size is not important when system reached to quasi-equilibrium stage. Could you please let me know your idea about the sensible size of the box when PBC is applied? I would be appreciated if you could introduce me a recent review about it? Best wishes Rasoul On Tue, May 7, 2013 at 5:24 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: If you don't want to simulate your droplet in a perfect vacuum then in most MD codes you have to use either PBC or walls. There are advantages and disadvantages to both. I'm not an expert but in my opinion PBC make more physical sense than walls provided the box is sensibly chosen, *however*, I am not an expert. I suggest that you consult the literature for a discussion of the merits of various boundary conditions for MD simulations of droplets. There will be many papers discussing it and I'd be shocked if there aren't several review articles as well. Richard On 07/05/13 14:50, Rasoul Nasiri wrote: Dear All, I just had a question regarding using the PBC for evaporation of clusters. Due to PBC the evaporated molecules again come back to drop (re-condensation). For me such a process is physically meaning less. Shall I ask a question from GMX users about this issue. How we can eliminated this unphysical process? Please ote that I'm not interest to use vacuum since vapour pressure of nanodrop is essential foR my MD simulation. Many thanks Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Calculation of Temperature of Cluster
Dear All, I tried to use g_clustsize_d program for estimation of temperature of cluster/nanodroplet but the temperature output file is empty. Could you comment where is the problem? Please note that I can get Temperature of system using g_energy_d but I'm interest to know cooling effect of nano-drop after evaporation. Best Rasoul -- 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] Calculation of Temperature of Cluster
Bellow is my command which I used: g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg Rasoul On Mon, Apr 8, 2013 at 2:04 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Dear All, I tried to use g_clustsize_d program for estimation of temperature of cluster/nanodroplet but the temperature output file is empty. Could you comment where is the problem? Not without seeing your command line. I'd be willing to guess that you either used an .xtc file (which does not store velocities) or a .trr that didn't save velocities (i.e. nstvout = 0). -Justin Please note that I can get Temperature of system using g_energy_d but I'm interest to know cooling effect of nano-drop after evaporation. Best Rasoul -- 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Calculation of Temperature of Cluster
Justin, Thanks for your comment. Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still encountering to empty file for temperature. Rasoul On Mon, Apr 8, 2013 at 2:10 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Bellow is my command which I used: g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg Then it is exactly what I said. Temperatures require velocities. Velocities are not stored in .xtc files and thus you can't extract any temperature information in this way. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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] Calculation of Temperature of Cluster
One suggestion, Is there any chance to retrieve trajectory of un-evaporated molecules using one of gromacs tools? Now I have a ndx file which show number of atoms stayed in drop, Which one is better? I mean if I can get trajectory (position+velocity) unevaporated molecules, I would be able estimate the temperature as well. Is it correct? Rasoul On Mon, Apr 8, 2013 at 2:30 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Justin, Thanks for your comment. Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still encountering to empty file for temperature. Can you please provide the gmxcheck output for the .trr file? I suppose there could be a bug, but we need to rule out a few things first. If g_clustsize still fails, you can get the output temperature from g_traj -ot, which appears to have a redundant function. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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
[gmx-users] Calculation of the Force on the center of bonds
Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these centers and those are only available for the center of C-H. So, I just wanted to know how calculation of force can be implemented by GROMACS in this case. Best wishes Rasoul -- 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] Calculation of the Force on the center of bonds
Dear Erik, Many thanks for your comment. The situation seems to be similar to TIP4P water model where the M site is located among the three other atoms. In my case, it's between the two C-H atoms. Could I ask you which parameters must be selected for these virtual sites? The interest molecule is n-alkane that have (2n+2) C-H bond. Is that make sense that I put the virtual sites there? Best Rasoul On Mon, Feb 11, 2013 at 5:33 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Try virtual sites constructions. On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote: Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these centers and those are only available for the center of C-H. So, I just wanted to know how calculation of force can be implemented by GROMACS in this case. Best wishes Rasoul -- 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 thewww 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] PBC for evaporation of droplets?
Dear all, I would like to ask you that using PBC for evaporation of droplets is necessary? Please note that the MD simulations are to be performed in vacuum. I checked the relevant references but in some of them PBC has been taken into account but in others not [for instance please see J.chem. phys. 125, 154508 (2006) and J. chem. phys. 134, 164309 (2011)]. I would be grateful if you can tell me advantages and disadvantages of PBC in evaporation of droplets in the vacuum. Best regards Rasoul -- 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] Evaporation Free Energy
Dear GMX users, I just wanted to know that it's possible one estimates Gibbs free energy of evaporation via following the solvation free energy scheme? I'm trying to obtain evaporation rate with using the value of G(evap.) for different hydrocarbon molecules at different temperatures. Any advice would be highly appreciated! Best Regards Rasoul -- 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] How can I maintain a distance of at least 0.5 nm from each other of solutes
Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Thanks for helping! Rasoul -- 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
Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes
Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? Rasoul On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear All, Hello I understand one can adjust distance of between solvent molecules by genbox command and -vdwd but I don't know, how do it between the solutes? Position your solutes using editconf -center, then add solvent. -Justin Thanks for helping! Rasoul -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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 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
Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes
Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the appropriate distances. Is it OK? Rasoul On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you could run a pulling simulation to separate your two species, but that requires substantially more work (and setup considerations) than the two or three quick editconf commands to properly build the system. Correction: you can use editconf -translate with appropriate index groups to separate your solutes. This will also imply that you haven't added solvent, which is the same thing as positioning the two solutes appropriately in the first place (with editconf -center, as I posted before). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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 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
Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes
Thanks for the information. Because of haven't satisfactory model from my co-solvent and I have to add it randomly along with the solvent by genbox -ci -nmol. the reason of this criteria relate to crash of system (solute+co-solvent+solvent) in the first step of simulation, because small distance between solute and co-solvents and co-solvents with themselves cause to rise of pressure. Rasoul . On Sat, Apr 17, 2010 at 6:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Hi, Thanks for the replies. Since I want to increase distance among co-solvents with themselves and with solutes, i must firstly fill the co-solvents along solutes and solvents after that i remove solvent, finally by edittconf -translate the co-solvents uniformally is distributed in the appropriate distances. Is it OK? Why bother adding solvent if you're just going to remove it? Here's what I would do: 1. Position solutes in the box with editconf -center 2. Add co-solvents (with a large value of -vdwd, I suppose) 3. Add solvent I don't fully grasp why the initial position of the co-solvents matters so precisely; you may have a hard time satisfying all of the simultaneous distance requirements. Everything is just going to diffuse around anyway during MD. Maybe you have some reason I'm not thinking of, but it's a potentially complicated problem to build. -Justin Rasoul On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Justin A. Lemkul wrote: rasoul nasiri wrote: Dear Justin, Hello again Thanks for the message. I want to increase the distance between solutes in simulation box before MD simulation. How can I do it? You can't. If you know you need a certain distance, that should be part of your planning :) I suppose you could run a pulling simulation to separate your two species, but that requires substantially more work (and setup considerations) than the two or three quick editconf commands to properly build the system. Correction: you can use editconf -translate with appropriate index groups to separate your solutes. This will also imply that you haven't added solvent, which is the same thing as positioning the two solutes appropriately in the first place (with editconf -center, as I posted before). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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 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
Re: [gmx-users] Martini Coarse Graining Segmentation Fault using g_fg2cg
Hi, It is better you plan this question in MARtini forum, there are experts that can answer this question! Please register in: http://md.chem.rug.nl/cgmartini/index.php/user-platform/login Rasoul On Thu, Jan 28, 2010 at 1:43 PM, Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de wrote: Dear Gromacs Users, I have performed the Martini Coarse Graining procedure for the simulation of two protein domains by using the two scripts atom2cg.awk and seq2itp.pl. Then I was able to perform my simulation of my coarse grained system. My problem is now to convert my final cg structure into an all atom structure. For this purpose I tried to use the tool g_fg2cg with the inputs containing my fine grained topology ,the coarse grained topology and my coarse grained structure file. But obviously all attempts to apply that tool ended up in a segmentation fault message. I also tried to convert my all atom structure into a cg structure which ended up with the same segmentation fault message. Could you give me some advice on that problem? Here is my screen output: Option Filename Type Description -pfg LOV1_LOV2.pdb.top InputTopology file -pcg martini_v2.0_example.top Input, Opt! Topology file -c lov1lov2_42ns_27.1.pdb InputGeneric trajectory: xtc trr trj gro g96 pdb -oout.gro Output Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -niceint 0 Set the nicelevel -nint 0 1: fg2cg transformation, 0: cg2fg transformation -watint 0 1: rewrites FG_CG water to true fg water; -rad real0.3 A radius for random atom insertion; calling cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -2.98e+00 # G96BONDS: 2738 # G96ANGLES: 3994 # PDIHS: 1465 # IDIHS: 1328 # LJ14: 4520 calling cpp... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours for Protein 1 Excluding 1 bonded neighbours for ProteinB 1 NOTE: System has non-zero total charge: -6.00e+00 Number of fg atoms 2696 Number of cg atoms 571 Reading frame 0 time 42000.004 1264673691 Segmentation fault When I applied this tool on the ubiquitin example I had another problem, but I did it in the same way as before. Here is the screen output: Option Filename Type Description -pfg 1ubq.top InputTopology file -pcg out3.top Input, Opt! Topology file -c 1UBQ.gro InputGeneric trajectory: xtc trr trj gro g96 pdb -oout.gro Output Generic structure: gro g96 pdb xml Option Type Value Description -- -[no]h bool no Print help info and quit -niceint 0 Set the nicelevel -nint 1 1: fg2cg transformation, 0: cg2fg transformation -watint 0 1: rewrites FG_CG water to true fg water; -rad real0.3 A radius for random atom insertion; calling cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 58 # G96BONDS: 766 # G96ANGLES: 1107 # PDIHS: 428 # IDIHS: 334 # LJ14: 1304 # SETTLE: 58 calling cpp... cpp: out3.top: Datei oder Verzeichnis nicht gefunden cpp: warning: '-x c' after last input file has no effect cpp: no input files cpp exit code: 256 Tried to execute: 'cpp -I/pc50417/pee18323/REVERSE_trans_gromacs/agromacs-reverse/share/top out3.top grompp605Sk3' The 'cpp' command is defined in the .mdp file processing topology... Number of fg atoms 934 Number of cg atoms 0 Reading frames from gro file 'UBIQUITIN', 934 atoms. Reading frame 0 time0.000 out.xtc Last frame 0 time0.000 Back Off! I just backed up out.gro to ./#out.gro.2# Cg structure computed ! In that case out.gro did not contain any atoms. Thanks for any suggestions! Best regards, Emanuel Peter -- 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 mailing list
Re: [gmx-users] workshop for Gromacs
Hi, please see: http://tfy.tkk.fi/soft/levi2010/ Rasoul On Thu, Jan 28, 2010 at 12:42 PM, oguz gurbulak gurbulako...@yahoo.comwrote: Dear Gromacs Developers, I'm intested in a workshop for Gromacs. Is there a workshop planned in 2010 ? Kind Regards, -- 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 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
Re: [gmx-users] solvent except water
Hi I want to use a solvent with two types molecules (for example linear and cyclic Glucose form). How can I fill box with them? I highly appreciate for advice given me! Best Regards Rasoul On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: leila karami wrote: Dear David in genbox command system solvated by water molecule by default. but I want solvent except water. leila karami OK, now I understand. You can give to genbox any solvent that you like, provided that each molecule consists of a single residue (the residue number is used to distinguish molecules). In the gromacs distribution there are a couple of other solvents present. Look in share/gromacs/top directory of your installation (or roll your own). -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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 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
Re: [gmx-users] do_dssp
Do you have a DSSP program on your system? If no, please install executable DSSP program from http://swift.cmbi.kun.nl/gv/dssp/ website. Rasoul On Wed, Jan 6, 2010 at 11:34 AM, leila karami karami.lei...@gmail.comwrote: Hi I apply following command: do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map but following error is came up: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddal9qL4 ddRvmyo0 /dev/null 2 /dev/null Any help will highly appreciated! -- 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 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
Re: [gmx-users] do_dssp
Then your executable has problem. Gromacs tool can not find DSSP for doing d_dssp. Do you put executable DSSP in the path of gromacs is installed? Rasoul. On Wed, Jan 6, 2010 at 11:58 AM, leila karami karami.lei...@gmail.comwrote: dear Rasoul I had executable dssp program, already. leila karami -- 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 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
Re: [gmx-users] do_dssp
yes. Could you perform do_dssp properly? Rasoul On Wed, Jan 6, 2010 at 1:05 PM, leila karami karami.lei...@gmail.comwrote: dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? -- 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 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
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information (%alpha-Helix, %beta-sheet and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.htmland another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html. Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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 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
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
Hi, Thank you for your quick reply. Is there another CGFF for this purpose that Gromacs can read it? What is your opinion about CG GO model? Kind regards Rasoul On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Justin, Thank you for your message. I have found some experimental evidence to suggest that the secondary structure information of protein how change during the reaction of the unfolding. In the other hand, I have percentage of the secondary structure information (%alpha-Helix, %beta-sheet and %Random coil) of the protein at different time of reaction. Could I perform CGMD simulation with MArtini force field for finding the denaturation mechanism of the protein properly? I would be extremely suspicious of any results you get. As you've been told before, secondary structure is a fixed aspect of a MARTINI CG simulation. Making changes is somewhat arbitrary and may lead to artifacts that you can't anticipate. Besides, if you only know percentages of secondary structure (from CD I assume?) then you don't really know the structures and sequences that are changing, do you? Net result: this particular CG model is probably not suitable for such a simulation. -Justin Best regards Rasoul On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: rasoul nasiri wrote: Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html http://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html . Is there difference between them? Maybe, but if you do sufficient equilibration, it probably won't matter. Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? No. This has been stated before - the awk script is explicitly for protein. And besides, each W CG particle corresponds to about four water molecules, so there is no trivial way to decide how to build the CG water system from spc216.gro. Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. You specify the secondary structure when building the initial topology. As you've been advised already, this fixed representation of secondary structure is going to be a major limitation of using the MARTINI force field for your simulations. How do you know that whatever alternate secondary structure you've applied is valid? If you have some experimental evidence to suggest that certain peptide regions convert between one form and another, that's fine, but how do you know that the pathway taken is not an artifact of your choice to abruptly impose a change in the topology? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin --gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/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 mailing listgmx-users@gromacs.org
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
Dear Cesar, Thank you for your reply, There are two different kind of water gro in this site (one of them is water.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html and another is water-1bar-303k.gro in : http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html . Is there difference between them? Can I build water.gro with coarse graining beads (P4) from spc216.gro with using atom2cg.awk script? Another question; How can I change secondary structure information during CGMD simulation, If I want to perform CGMD simulation for finding of the folding/unfolding mechanism in proteins completely? Because Martini CGFF consider fix it. Cheers Rasoul On Fri, Dec 18, 2009 at 9:02 PM, César Ávila clav...@gmail.com wrote: For a detailed description of how to set up protein simulation, I recommend you to read the Martini Tutorial on http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.htmlhttp://md.chem.rug.nl/%7Emarrink/MARTINI/Tutorial.html there you will find step by step instructions along with some explanations of what you are actually doing. In this case you only want to build a water box around your protein. For that you will use editconf and a vdw distance of 0.19. Regards Cesar 2009/12/17 rasoul nasiri nasiri1...@gmail.com yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have contribution to the denaturation mechanism. My question is about vdwd in beads of water. Is it OK if I select distances of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to reconstruct the system in smaller vdw distance of the water beads for doing my purpose. and Which commands of Gromacs can do it? Best regards Rasoul On Thu, Dec 17, 2009 at 5:03 PM, César Ávila clav...@gmail.com wrote: I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. 2009/12/17 rasoul nasiri nasiri1...@gmail.com Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? Rasoul On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. 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/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 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 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 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
[gmx-users] How can I reconstruct the system in CGMD simulation?
greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? I have to switch back to the smaller radius afterward, Is it correct? if yes, How can I do it? I tried with editconf but could not. Best regards, Rasoul -- 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
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? Rasoul On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. 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/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 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
Re: [gmx-users] How can I reconstruct the system in CGMD simulation?
yes, I know there will be limitation for modeling of Folding/Unfolding proteins with MARtini CGFF if I want to look at complete folding/unfolding mechanism of proteins but I want to find out localized regions of the protein (e.g. the C- or N-termini) that they have contribution to the denaturation mechanism. My question is about vdwd in beads of water. Is it OK if I select distances of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to reconstruct the system in smaller vdw distance of the water beads for doing my purpose. and Which commands of Gromacs can do it? Best regards Rasoul On Thu, Dec 17, 2009 at 5:03 PM, César Ávila clav...@gmail.com wrote: I suggest you read the original paper for Martini Protein FF. I think it is not suitable for your purpouse. 2009/12/17 rasoul nasiri nasiri1...@gmail.com Hi, My purpose is finding of denaturation mechanism of proteins with MArtini CGFF by Gromacs. I mean after filling box in which there are beads of protein from water beads with suitable van der wall distance (larger than 0.105nm), when I want to start production phase, first switch back to the smaller radius of van der waals of the water beads, then I will continue CGMD simulation. Is it possible I reduce this radius? Which commands of Gromacs suit can do it? Rasoul On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: rasoul nasiri wrote: greetings GMX users, When I use genbox command for filling solvent in CGMD simulation with Gromacs suit, I must use a larger van der Waals distance to avoid crashes. when I use default value (0.105nm), system will crash. Which distance is suitable for performing CGMD simulation. I used 0.15 or 0.2nm as distances. Are those OK? Read up on your forcefield and find out how large the particles tend to be. It only has to be good enough, not perfect. I have to switch back to the smaller radius afterward, Is it correct? Changing what for what purpose? if yes, How can I do it? I tried with editconf but could not. I don't know what you mean. 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/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 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 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 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] Denaturation of Proteins by MARTINI Coarse-Graining Forse Field
Dear GMX users, Hi I'm working on denaturation of proteins with MARTINI CGFF by Gromacs suit. according to this paper (J. Chem. Theory and Comput. 2008, 4, 819–834) I undestand there is a limitation for modeling of folding and unfolding with MARITI CGFF for systems in which the folding and unfolding of secondary structures are playing a substantial role are therefore not suitable for modeling with current CG force field. since I perform CGMD simulation on tertiary structure, is there this limitation on my system or no? If your question is positive, Is there an improved version of MARTINI CGFF for doing it? Can I use Gō model for resolve of this problem? What is your idea about this problem? I'm looking forward to hearing from you about this matter! Beast Regards Rasoul -- 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
