[gmx-users] rdf problem
Dear all, I am simulating a binary system of two non mixing components (5CB and water using version 4-0-3; the whole equilibrated trajectory is about 300ns). I want to calculate the rdf of the centers of mass of 5CB using the command g_rdf -f traj300.xtc -rdf mol_com -o rdf_com_300.xvg -noxvgr. The problem is that the rdf I am getting does not approach one at long distances. Is there a way to correct that? I have the same problem, with all rdfs, and also when I compute the rdfs for a lipid bilayer (DPPC-water)... I think it has to do with the way that the normalization is done, because the ones that are calculated for a one component system (i.e. bulk 5CB) are normal (they do approach one). Thank you, Antonia Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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] rdf problem
> Date: Tue, 9 Mar 2010 10:39:01 +0100 > From: er...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] rdf problem > > Antonia V. skrev: > > Dear all, > > > > I am simulating a binary system of two non mixing components (5CB and > > water using version 4-0-3; the whole equilibrated trajectory is about > > 300ns). > > I want to calculate the rdf of the centers of mass of 5CB using the > > command > > g_rdf -f traj300.xtc -rdf mol_com -o rdf_com_300.xvg -noxvgr. > > The problem is that the rdf I am getting does not approach zero at > > long distances. Is there a way to correct that? > > > > Thank you in advance for your help, > > Antonia > > > > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign > > up now. <https://signup.live.com/signup.aspx?id=60969> > > But it should not, should it? The rdf normally approaches one for long > distances. > Yes! Sorry, it was a typo. I meant that it doesn't approach one.. > --- > Erik Marklund, PhD student > Laboratory of Molecular Biophysics, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:+46 18 471 4537fax: +46 18 511 755 > er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys > > -- > 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 _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- 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] rdf problem
Dear all, I am simulating a binary system of two non mixing components (5CB and water using version 4-0-3; the whole equilibrated trajectory is about 300ns). I want to calculate the rdf of the centers of mass of 5CB using the command g_rdf -f traj300.xtc -rdf mol_com -o rdf_com_300.xvg -noxvgr. The problem is that the rdf I am getting does not approach zero at long distances. Is there a way to correct that? Thank you in advance for your help, Antonia _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] rdf not equal to one
Dear all, I am simulating a two component system (which form two completely separated phases) and I want to calculate the g(r) of the centers of mass of the one component. Using the command, g_rdf -f traj.xtc -rdf mol_com I get an rdf which doesn't obtain the value one at long distances. How can I change that? thank you for your help, Antonia _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] (no subject)
Dear all, I am simulating a two component system and I want to calculate the g(r) of the centers of mass of the one component. Using the command, g_rdf -f traj.xtc -rdf mol_com I get an rdf which doesn't obtain the value one at long distances. How can I change that? thank you for your help, Antonia _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] LJ scaling and EnerPress correction
> > I am trying to simulate a two component system, and I would like to ask > > you the two following questions: > > > > 1) Is it possible to use a different scaling factor (for the LJ and the > > electrostatics) for each component? > > Not natively. How would you like to treat non-bonded interactions > between atoms belonging to different components? I am still trying to figure that out. According to the force fields I am using for the bulk systems of the two components are applying different scaling factors. > > 2) Is it possible to use energy and pressure correction only for the one > > of the two components and not for the other? > > No. Why would you want to do this? Because the force fields that I am using to describe my two-component system, are different in this aspect. The one of them was "designed" using energy and pressure correction and the other one not. Thank you for your reply Antonia _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009-- 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] LJ scaling and EnerPress correction
Dear all, I am trying to simulate a two component system, and I would like to ask you the two following questions: 1) Is it possible to use a different scaling factor (for the LJ and the electrostatics) for each component? 2) Is it possible to use energy and pressure correction only for the one of the two components and not for the other? Thank you for your help, Antonia Keep your friends updated— even when you’re not signed in. _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009-- 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] LJ scaling and EnerPress correction
Dear all, I am trying to simulate a two component system, and I would like to ask you the two following questions: 1) Is it possible to use a different scaling factor (for the LJ and the electrostatics) for each component? 2) Is it possible to use energy and pressure correction only for the one of the two components and not for the other? Thank you in advance for your help, Antonia _ Keep your friends updated—even when you’re not signed in. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_5:092010___ 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] (no subject)
Unfortunately, it' s the only way I can do it, since I want two completely separated phases. With the tools provided by GROMACS I get a mixture, is there a way to get a box with two separated phases? Antonia _ Show them the way! Add maps and directions to your party invites. http://www.microsoft.com/windows/windowslive/products/events.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
FW: [gmx-users] (no subject)
> Date: Fri, 8 May 2009 19:38:41 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] (no subject) > > Antonia V. wrote: > > Dear all, > > > > I am trying to simulate a water-liquid crystal system. My initial is box > > is creating by merging two well equilibrated boxes of water and LC. > > After a steep simulation of about 1,000,000 steps I try to do an md > > simulation but I get the error > > "Water molecule starting at atom 9103 can not be settled. > > Check for bad contacts and/or reduce the timestep" > > In order to get the simulation running I have to use a tiny timestep > > (0.1). > > Have a look at the region around atom 9103 in case you can deduce a > physical reason for large forces that would make applying constraints > difficult. > > Otherwise, consider alternative approaches to generating your initial > structure. It's not clear to me that whatever you mean by "merging" is > reasonable. > > Mark > ___ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Show them the way! Add maps and directions to your party invites. http://www.microsoft.com/windows/windowslive/products/events.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hi, I just put one box on top of the other in order to make my new system. I use no constraints for the system, and I can't figure out the problem. It seems that the water molecules of the new system are getting crazy... Antonia _ Windows Live™: Keep your life in sync. Check it out! http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t1_allup_explore_012009___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Dear all, I am trying to simulate a water-liquid crystal system. My initial is box is creating by merging two well equilibrated boxes of water and LC. After a steep simulation of about 1,000,000 steps I try to do an md simulation but I get the error "Water molecule starting at atom 9103 can not be settled. Check for bad contacts and/or reduce the timestep" In order to get the simulation running I have to use a tiny timestep (0.1). Any ideas about how I can solve this problem? Thanks in advance Antonia _ More than messages–check out the rest of the Windows Live™. http://www.microsoft.com/windows/windowslive/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] md error message
Dear all, I am trying to do an md simulation of a system consiting of water and liquid crystalline molecules, starting from a random initial configuration. After some energy minimization if I try to do an NVT simulation (I use the VERSION 4.0.3) I get the error t = 0.000 ps: Water molecule starting at atom 8728 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates step 0 Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR) Failing at addr:0x1005feee0 [0] func:/usr/lib64/openmpi/libopal.so.0 [0x3262d21dc5] [1] func:/lib64/tls/libpthread.so.0 [0x326360c4f0] [2] func:mdrun(gmx_pme_do+0x16b8) [0x4ba1c8] [3] func:mdrun(do_force_lowlevel+0x118a) [0x48f1da] [4] func:mdrun(do_force+0xdbd) [0x4cb51d] [5] func:mdrun(do_md+0x31fa) [0x4328aa] [6] func:mdrun(mdrunner+0x8ad) [0x42eb9d] [7] func:mdrun(main+0x3e5) [0x435095] [8] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3262f1c3fb] [9] func:mdrun [0x41a29a] *** End of error message *** Segmentation fault The time step I am using is 0.002, but even when I try a smaller one I get the same error. The water molecules are not flexible and I am not using any constraints for the LC. Attached you can find my mdp file. Any ideas? Thanks Antonia _ More than messages–check out the rest of the Windows Live™. http://www.microsoft.com/windows/windowslive/ lc5cbNPT.mdp Description: Binary data ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] md.mdp query
At the beginning of your md.mdp file you will see the following: ; RUN CONTROL PARAMETERS integrator = steep With this command you ask GROMACS to energy minimize your system by steepest descent. If you want to run a md simulation you will have to change the intergrator to md. You can read this, and more, in details in the manual. Good luck Antonia Date: Tue, 7 Apr 2009 17:16:03 +0530 From: bissoyi.akala...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] md.mdp query hello gromacs, i want to know the changes to be done in md.mdp files for 10 ns. i am trying to run it but it's showing the following message. Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 1000 Step=0, Dmax= 1.0e-02 nm, Epot= -5.01412e+06 Fmax= 3.66197e+03, atom= 4032 Step=2, Dmax= 5.0e-03 nm, Epot= -5.01438e+06 Fmax= 2.17491e+04, atom= 4032 Step=3, Dmax= 6.0e-03 nm, Epot= -5.01456e+06 Fmax= 9.13099e+03, atom= 4032 Step=5, Dmax= 3.6e-03 nm, Epot= -5.01468e+06 Fmax= 9.44298e+03, atom= 4032 Step= 10, Dmax= 2.7e-04 nm, Epot= -5.01470e+06 Fmax= 8.04093e+03, atom= 4032 Step= 11, Dmax= 3.2e-04 nm, Epot= -5.01472e+06 Fmax= 6.36864e+03, atom= 4032 Step= 12, Dmax= 3.9e-04 nm, Epot= -5.01474e+06 Fmax= 4.35105e+03, atom= 4032 Step= 14, Dmax= 2.3e-04 nm, Epot= -5.01476e+06 Fmax= 3.13319e+03, atom= 4032 Step= 16, Dmax= 1.4e-04 nm, Epot= -5.01478e+06 Fmax= 2.39737e+03, atom= 4032 Step= 18, Dmax= 8.4e-05 nm, Epot= -5.01478e+06 Fmax= 1.98224e+03, atom= 4032 Step= 21, Dmax= 2.5e-05 nm, Epot= -5.01479e+06 Fmax= 1.88313e+03, atom= 4034 Step= 22, Dmax= 3.0e-05 nm, Epot= -5.01479e+06 Fmax= 1.68824e+03, atom= 4032 Step= 23, Dmax= 3.6e-05 nm, Epot= -5.01479e+06 Fmax= 1.50693e+03, atom= 4032 Step= 25, Dmax= 2.2e-05 nm, Epot= -5.01479e+06 Fmax= 1.39532e+03, atom= 4032 Step= 26, Dmax= 2.6e-05 nm, Epot= -5.01480e+06 Fmax= 1.30313e+03, atom= 4032 Step= 27, Dmax= 3.1e-05 nm, Epot= -5.01481e+06 Fmax= 1.12668e+03, atom= 4034 Step= 28, Dmax= 3.8e-05 nm, Epot= -5.01482e+06 Fmax= 9.41676e+02, atom= 4034 Step= 30, Dmax= 2.3e-05 nm, Epot= -5.01483e+06 Fmax= 8.67996e+02, atom= 4032 Step= 31, Dmax= 2.7e-05 nm, Epot= -5.01483e+06 Fmax= 6.80316e+02, atom= 4034 Step= 32, Dmax= 3.2e-05 nm, Epot= -5.01484e+06 Fmax= 5.66923e+02, atom= 4034 Step= 33, Dmax= 3.9e-05 nm, Epot= -5.01485e+06 Fmax= 3.30411e+02, atom= 1881 Step= 35, Dmax= 2.3e-05 nm, Epot= -5.01487e+06 Fmax= 3.12606e+02, atom= 1881 Step= 37, Dmax= 1.4e-05 nm, Epot= -5.01488e+06 Fmax= 3.86990e+02, atom= 92925 Step= 38, Dmax= 1.7e-05 nm, Epot= -5.01489e+06 Fmax= 3.70596e+02, atom= 286823 Step= 40, Dmax= 1.0e-05 nm, Epot= -5.01489e+06 Fmax= 4.65471e+02, atom= 142601 Step= 41, Dmax= 1.2e-05 nm, Epot= -5.01490e+06 Fmax= 4.51394e+02, atom= 155810 Step= 43, Dmax= 7.3e-06 nm, Epot= -5.01490e+06 Fmax= 6.46500e+02, atom= 167601 Step= 47, Dmax= 1.1e-06 nm, Epot= -5.01490e+06 Fmax= 4.30994e+03, atom= 214498 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up traj.trr to ./#traj.trr.12# Back Off! I just backed up md.pdb to ./#md.pdb.8# Steepest Descents converged to machine precision in 48 steps, but did not reach the requested Fmax < 10. Potential Energy = -5.0149030e+06 Maximum force = 6.4650037e+02 on atom 167601 Norm of force = 7.3590344e+04 Kindly help me in this regard.I am attaching md.mdp file in which i have made the changes. -- akalabya N.I.T.Rourkela _ Show them the way! Add maps and directions to your party invites. http://www.microsoft.com/windows/windowslive/products/events.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] (no subject)
I switched to v-rescale for the thermostat and things look normal! Thanks for the help Antonia > Date: Wed, 1 Apr 2009 12:11:47 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] (no subject) > > > > Antonia V. wrote: > > > 1. A description of your system > > > > I have a system of 250 5CB molecules (it is a liquid crystal) which > > means 4750 atoms. > > > > > 2. Anything else that was printed to screen or the .log file (that's > > where the > > > real error message will appear) > > > > On the screen the message was > > [compute-0-4:01361] *** Process received signal *** > > [compute-0-4:01361] Signal: Segmentation fault (11) > > [compute-0-4:01361] Signal code: Address not mapped (1) > > [compute-0-4:01361] Failing at address: 0x1913c280 > > [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] > > [compute-0-4:01361] [ 1] mdrun [0x6a46cd] > > [compute-0-4:01361] *** End of error message *** > > Segmentation fault > > > > and the last thing that was written in the md.log file is > > > >Step Time Lambda > > 00.00.0 > > > > Grid: 8 x 8 x 8 cells > >Energies (kJ/mol) > >Bond AngleProper Dih.LJ (SR) Coulomb (SR) > > 3.12078e+037.44768e+045.19128e+03 -1.67708e+04 -1.07965e+03 > >Coul. recip. PotentialKinetic En. Total EnergyTemperature > >-6.75318e+035.81852e+042.02196e+015.82054e+043.41383e-01 > > Pressure (bar) > >-2.55714e+03 > > > > Your potential energy has spiked to a very large value. That indicates you > still have some bad contacts in the system. > > > > 3. What happened in the EM procedure? > > After the EM (steep) the forces were minimized to the desired accuracy > > (Tolerance (Fmax) = 1.0e+02) > > > > Was the potential reasonable? See above. > > > > 4. What .mdp parameters you are using > > I use a time step of 2fs, PME for the electrostatics, a quite large > > cut-off (1.2), the nose-hoover thermostat (340K) > > > > Well, these are not all of your parameters, surely (it's best to post your > whole > .mdp file). If you are going for 340 K, you can see from your .log file that > the temperature is actually 0.34 K. Are you doing some sort of annealing > protocol? Again, it's best to give complete information :) > > Nose-Hoover is a poor choice for initial equilibration, if this is what you > are > doing. It allows greater temperature fluctuation. Start with Berendsen or > V-rescale for some time, then switch to N-H when collecting your "real" data, > if > N-H is your choice for thermostat. > > Is a .trr ever output? If it is, you can view the trajectory to see where > things are going wrong. If you don't get a .trr, then set nstxout = 1 in the > .mdp file to hopefully get a frame or two of where the problem may lie. > > -Justin > > > > 5. Which Gromacs version you are using > > > > I use GROMACS 4.0.3 > > > > Thank you > > Antonia > > > > > Date: Wed, 1 Apr 2009 06:39:17 -0400 > > > From: jalem...@vt.edu > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] (no subject) > > > > > > > > > > > > Antonia V. wrote: > > > > Hello, > > > > > > > > I am trying to simulate a system at the NVT ensemble, but after a few > > > > steps I get the error > > > > [compute-0-4:01361] *** Process received signal *** > > > > [compute-0-4:01361] Signal: Segmentation fault (11) > > > > [compute-0-4:01361] Signal code: Address not mapped (1) > > > > [compute-0-4:01361] Failing at address: 0x1913c280 > > > > [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] > > > > [compute-0-4:01361] [ 1] mdrun [0x6a46cd] > > > > [compute-0-4:01361] *** End of error message *** > > > > Segmentation fault > > > > > > > > Any ideas what this means?? > > > > > > > > > > Given this information, no. Segmentation faults are difficult to pin > > down, > > > anyway, but if you want help, you'll have to provide more useful > > information: > > > > > > 1. A description of your system > > > 2. Anything else that was printed to screen or the .log file (that's > >
RE: [gmx-users] (no subject)
> 1. A description of your system I have a system of 250 5CB molecules (it is a liquid crystal) which means 4750 atoms. > 2. Anything else that was printed to screen or the .log file (that's where > the > real error message will appear) On the screen the message was [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault and the last thing that was written in the md.log file is Step Time Lambda 00.00.0 Grid: 8 x 8 x 8 cells Energies (kJ/mol) Bond AngleProper Dih.LJ (SR) Coulomb (SR) 3.12078e+037.44768e+045.19128e+03 -1.67708e+04 -1.07965e+03 Coul. recip. PotentialKinetic En. Total EnergyTemperature -6.75318e+035.81852e+042.02196e+015.82054e+043.41383e-01 Pressure (bar) -2.55714e+03 > 3. What happened in the EM procedure? After the EM (steep) the forces were minimized to the desired accuracy (Tolerance (Fmax) = 1.0e+02) > 4. What .mdp parameters you are using I use a time step of 2fs, PME for the electrostatics, a quite large cut-off (1.2), the nose-hoover thermostat (340K) > 5. Which Gromacs version you are using I use GROMACS 4.0.3 Thank you Antonia > Date: Wed, 1 Apr 2009 06:39:17 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] (no subject) > > > > Antonia V. wrote: > > Hello, > > > > I am trying to simulate a system at the NVT ensemble, but after a few > > steps I get the error > > [compute-0-4:01361] *** Process received signal *** > > [compute-0-4:01361] Signal: Segmentation fault (11) > > [compute-0-4:01361] Signal code: Address not mapped (1) > > [compute-0-4:01361] Failing at address: 0x1913c280 > > [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] > > [compute-0-4:01361] [ 1] mdrun [0x6a46cd] > > [compute-0-4:01361] *** End of error message *** > > Segmentation fault > > > > Any ideas what this means?? > > > > Given this information, no. Segmentation faults are difficult to pin down, > anyway, but if you want help, you'll have to provide more useful information: > > 1. A description of your system > 2. Anything else that was printed to screen or the .log file (that's where > the > real error message will appear) > 3. What happened in the EM procedure? > 4. What .mdp parameters you are using > 5. Which Gromacs version you are using > > -Justin > > > Thank you > > Antonia > > > > > > What can you do with the new Windows Live? Find out > > <http://www.microsoft.com/windows/windowslive/default.aspx> > > > > > > > > > > ___ > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > 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://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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ More than messages–check out the rest of the Windows Live™. http://www.microsoft.com/windows/windowslive/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hello, I am trying to simulate a system at the NVT ensemble, but after a few steps I get the error [compute-0-4:01361] *** Process received signal *** [compute-0-4:01361] Signal: Segmentation fault (11) [compute-0-4:01361] Signal code: Address not mapped (1) [compute-0-4:01361] Failing at address: 0x1913c280 [compute-0-4:01361] [ 0] /lib64/libpthread.so.0 [0x32b340de70] [compute-0-4:01361] [ 1] mdrun [0x6a46cd] [compute-0-4:01361] *** End of error message *** Segmentation fault Any ideas what this means?? Thank you Antonia _ Drag n’ drop—Get easy photo sharing with Windows Live™ Photos. http://www.microsoft.com/windows/windowslive/products/photos.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] How to calculate the dihedral angle variations ???
Did you try g_angle?? Antonia Date: Wed, 1 Apr 2009 11:35:29 +0530 From: venkat...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] How to calculate the dihedral angle variations ??? Hi Everyone ! How can i see the variations in the "Cβ-S-S-Cβ" (Disulfide bridge) dihedral angle during a simulation ? Thanks in advance Cheers from Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD _ More than messages-check out the rest of the Windows LiveT. http://www.microsoft.com/windows/windowslive/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] (no subject) - fluctuations
artificially small??? I think I will have to read some things about Berendsen and PR. Thanks Antonia > Date: Tue, 24 Mar 2009 11:09:07 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] (no subject) - fluctuations > > Antonia V. wrote: > > Hello, > > > > I am interested mainly in the density. > > When using parinello-rahman and nose-hoover the fluctuations are > > approximately +/- 8. But when I am using Berendsen it falls to +/- 3. > > I wanted to know if there is a way to reduce the fluctuation width of > > the first case. > > The density fluctuations in Berendsen are artificially small, so PR ones > should be more realistic. This is important when computing properties > like compressibility. > > > > > Antonia > > > > > Date: Tue, 24 Mar 2009 09:49:45 +0100 > > > From: sp...@xray.bmc.uu.se > > > To: gmx-users@gromacs.org > > > Subject: Re: [gmx-users] (no subject) - fluctuations > > > > > > Antonia V. wrote: > > > > Hello, > > > > > > > > So a I can either increase my system size or do some post > > > > precessing-smoothing... > > > > > > If you elaborate on which properties you are interested in it may be > > > possible to come up with more tips. > > > > > > > > Thanks for the ideas > > > > Antonia > > > > > > > > > Date: Tue, 24 Mar 2009 11:39:19 +1100 > > > > > From: dallas.war...@pharm.monash.edu.au > > > > > Subject: RE: [gmx-users] (no subject) - fluctuations > > > > > To: gmx-users@gromacs.org > > > > > > > > > > > > Is there a way to reduce the fluctuations of the properties > > > > > > calculated > > > > > > > with g_energy? > > > > > > > > > > > Fluctuations scale as 1/sqrt(N) where N is the number of > > > > > > molecules. So > > > > > > the answer is yes. > > > > > > > > > > Depending on what you actually want to do, some smoothing of the data > > > > > may be what you are after. One way of doing this is taking some > > points > > > > > before and after a time, then averaging them all together. > > > > > > > > > > Catch ya, > > > > > > > > > > Dr. Dallas Warren > > > > > Department of Pharmaceutical Biology and Pharmacology > > > > > Pharmacy and Pharmaceutical Sciences, Monash University > > > > > 381 Royal Parade, Parkville VIC 3010 > > > > > dallas.war...@pharm.monash.edu.au > > > > > +61 3 9903 9167 > > > > > - > > > > > When the only tool you own is a hammer, every problem begins to > > resemble > > > > > a nail. > > > > > ___ > > > > > gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > > > Get news, entertainment and everything you care about at Live.com. > > Check > > > > it out! <http://www.live.com/getstarted.aspx > > > > > > > > > > > > > > > > > > > > > > > ___ > > > > gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > -- > > > David van der Spoel, Ph.D., Prof
RE: [gmx-users] (no subject) - fluctuations
Hello, I am interested mainly in the density. When using parinello-rahman and nose-hoover the fluctuations are approximately +/- 8. But when I am using Berendsen it falls to +/- 3. I wanted to know if there is a way to reduce the fluctuation width of the first case. Antonia > Date: Tue, 24 Mar 2009 09:49:45 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] (no subject) - fluctuations > > Antonia V. wrote: > > Hello, > > > > So a I can either increase my system size or do some post > > precessing-smoothing... > > If you elaborate on which properties you are interested in it may be > possible to come up with more tips. > > > > Thanks for the ideas > > Antonia > > > > > Date: Tue, 24 Mar 2009 11:39:19 +1100 > > > From: dallas.war...@pharm.monash.edu.au > > > Subject: RE: [gmx-users] (no subject) - fluctuations > > > To: gmx-users@gromacs.org > > > > > > > > Is there a way to reduce the fluctuations of the properties > > > > calculated > > > > > with g_energy? > > > > > > > Fluctuations scale as 1/sqrt(N) where N is the number of > > > > molecules. So > > > > the answer is yes. > > > > > > Depending on what you actually want to do, some smoothing of the data > > > may be what you are after. One way of doing this is taking some points > > > before and after a time, then averaging them all together. > > > > > > Catch ya, > > > > > > Dr. Dallas Warren > > > Department of Pharmaceutical Biology and Pharmacology > > > Pharmacy and Pharmaceutical Sciences, Monash University > > > 381 Royal Parade, Parkville VIC 3010 > > > dallas.war...@pharm.monash.edu.au > > > +61 3 9903 9167 > > > - > > > When the only tool you own is a hammer, every problem begins to resemble > > > a nail. > > > ___ > > > gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > Get news, entertainment and everything you care about at Live.com. Check > > it out! <http://www.live.com/getstarted.aspx > > > > > > > > > > > ___ > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > 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.se sp...@gromacs.org http://folding.bmc.uu.se > ___ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] (no subject) - fluctuations
Hello, So a I can either increase my system size or do some post precessing-smoothing... Thanks for the ideas Antonia > Date: Tue, 24 Mar 2009 11:39:19 +1100 > From: dallas.war...@pharm.monash.edu.au > Subject: RE: [gmx-users] (no subject) - fluctuations > To: gmx-users@gromacs.org > > > > Is there a way to reduce the fluctuations of the properties > > calculated > > > with g_energy? > > > Fluctuations scale as 1/sqrt(N) where N is the number of > > molecules. So > > the answer is yes. > > Depending on what you actually want to do, some smoothing of the data > may be what you are after. One way of doing this is taking some points > before and after a time, then averaging them all together. > > Catch ya, > > Dr. Dallas Warren > Department of Pharmaceutical Biology and Pharmacology > Pharmacy and Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble > a nail. > ___ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hello, Is there a way to reduce the fluctuations of the properties calculated with g_energy? Thanks Antonia _ Drag n’ drop—Get easy photo sharing with Windows Live™ Photos. http://www.microsoft.com/windows/windowslive/products/photos.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_principal
Hello, sorry to ask again, but I wander if the output files (axis1.dat,axis2.dat and axis3.dat) of the g_principal program refer to Ixx, Ixy, Ixz, Iyx, Iyy, Iyz, Izx, Izy, Izz components respectively. Thank you Antonia _ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Questions About Gromacs
> Date: Thu, 19 Mar 2009 11:51:51 +0800 > From: xouy...@uvm.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] Questions About Gromacs > > Hi, there are 3 questions I want to ask. > > 1. I run the md from the pdb file successfully and get a .trr trajectory > file. But when I load the .trr file in VMD, there is just 1 frame. I > have 1000 steps and want to have every step as a frame. How can I do this? You should specify in your mdp file how often you want to store data in the trr file (every how many steps) Antonia > 2. Since I do signal processing, I want to do wavelet-based coarse > graining on the protein model. Then the big question is how can I > introduce the wavelet into gromacs? > > 3. I want to stretch the protein, how can I do this in Gromacs? Should I > do something with the .mdp file? > > Thanks again. I really look forward to someone's help. > > Xi > ___ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Show them the way! Add maps and directions to your party invites. http://www.microsoft.com/windows/windowslive/products/events.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] inertia
Hello, I want to calculate the moments of inertia of a system of liquid crystals. Using the tool g_gyrate I get 5 values. The three last values are called I1, I2 and I3. I suppose that they are Ixx, Iyy and Izz respectively. Is that correct? What about the second column which is called Itot. What is that? And about the units that are used for the components of I, a.m.u. nm\S2\N.. N is the Avogadro number? And what is S2?? And something else. When using g_principal I get three output .dat files 1, 2, 3. Does axis1.dat refer to Ixx, Ixy, Ixz, axis2.dat to Iyx, Iyy, Iyz etc? Thank you for your help Antonia _ Drag n’ drop—Get easy photo sharing with Windows Live™ Photos. http://www.microsoft.com/windows/windowslive/products/photos.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] center of mass
Thank you From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] center of mass Date: Mon, 16 Mar 2009 17:56:16 +0100 On Mar 16, 2009, at 5:51 PM, Antonia V. wrote:Hello, I am wondering if there is a tool implemented in GROMACS that computes the coordinates of the center of mass of each molecule of a simulation box. g_traj -f traj.xtc -com Thank you Antonia Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! Try it! ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Drag n’ drop—Get easy photo sharing with Windows Live™ Photos. http://www.microsoft.com/windows/windowslive/products/photos.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] center of mass
Hello, I am wondering if there is a tool implemented in GROMACS that computes the coordinates of the center of mass of each molecule of a simulation box. Thank you Antonia _ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
