[gmx-users] on g_rms analysis
Dear All, Suppose I have done a 5-ns production MD, I want to analysis the rmsd from 1 to 3 ns, will you please tell me the corresponding g_rms command? Cheers, Acoot-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] on g_rms analysis
On 10/04/2012 4:59 PM, Acoot Brett wrote: Dear All, Suppose I have done a 5-ns production MD, I want to analysis the rmsd from 1 to 3 ns, will you please tell me the corresponding g_rms command? g_rms has options that allow you to select the start and finish time for the analysis. Look them up for yourself in g_rms -h. This existence of this mailing list is not an excuse for avoiding attempting to find your own solutions. You want people to be still willing to help you when you run into a problem that is not just a simple exercise in reading the available documentation :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] SS bond forcing
Here is what I have done: First, I created the .gro file with the command line: pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing Then, I added at the end of my test.top file the following lines (I double checked the atom numbers): [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 37 140 1 0 1 0.19 0.21 0.22 1 then, I done: editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0 and finally get my new pdb file with: editconf -f test-min.gro -o test-min.pdb But it didn't seemed it had make the two sufur atom closer than if I didn't add the distance_restrain in the top file. Did I do something wrong? Thank You. Pierre THEVENET Pierre THEVENET wrote: Thank you for your help, I tried to do as indicated in the link to send to me, but it seems that it didn't change anything. Could you show me an example, to better understand what I am doing wrong? It would be better for you to show us what you tried, along with whatever evidence suggests the restraints didn't work. There are several examples provided in the manual, so the only things I would post as examples are already available. -Justin Thank you Pierre THEVENET Le 06/04/2012 17:19, Justin A. Lemkul a écrit : pitheve...@free.fr wrote: Dear gmx users, I try to use gmx to make some minimization. Unfortunatly, I have some SS bonds which are not formed in my PDB because the S-S atoms are too far away to connect to each other. I saw at that page : http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds that it is possible to force GROMACS to make bonds with sulfur atoms by adding a distant constrains between the atoms. Note that constraints and restraints are different. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints But I didn't understand in which file it should be inserted and at which step. Can you help me? If you want to restrain S-S distances to force a more amenable geometry for disulfide formation, what you need are distance restraints in the .top: http://www.gromacs.org/Documentation/How-tos/Distance_Restraints Refer to the manual section and figures cited on that page for more information. -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/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] Problem with g_dipoles and SPCE water
Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant (e_sim=109.713) looks very different from experimental (e_exp=78) and reported values for SPCE (e_paper=70). I put the command line and the output below. Gromacs 4.5.3, SPC/E water, 20ns, NPT, 300K, 1bar g_dipoles -corr total -c dipoles -f md_20ns.xtc -s md_20ns.tpr -b 0 -e 2 #== Using 5 as mu_max and -1 as the dipole moment. WARNING: EpsilonRF = 0.0, this really means EpsilonRF = infinity Selected 0: 'System' There are 1024 molecules in the selection Using Volume from topology: 30.2049 nm3 Average volume over run is 30.2103 t0 0, t 2, teller 10001 Dipole moment (Debye) - Average = 2.4883 Std. Dev. = 0.1342 Error = 0. The following averages for the complete trajectory have been calculated: Total M_x = 1.45986 Debye Total M_y = 5.71202 Debye Total M_z = 3.39196 Debye Total M_x2= 10964.8 Debye2 Total M_y2= 10794.4 Debye2 Total M_z2= 10762.4 Debye2 Total |M|^2 = 32521.6 Debye2 Total | M|^2 = 46.2638 Debye2 |M|^2 - | M|^2 = 32475.4 Debye2 Finite system Kirkwood g factor G_k = 5.12208 Infinite system Kirkwood g factor g_k = 3.43028 Epsilon = 109.713 #== I would be really grateful if anybody could point me to my error. I attached my .mdp file in case the error lies there. Best regards Tom ;== run control === integrator = md tinit = 0 dt = 0.002 ; time step [ps] nsteps = 1000 ; number of steps comm_mode = Linear; Remove center of mass translation nstcomm = 10; reset c.o.m. motion ;== Output control === nstxout = 1000 ; write coords nstvout = 1000 ; write velocities nstfout = 0 ; do NOT write forces nstlog = 1000 ; print to logfile nstenergy = 1000 nstxtcout = 1000 ; write coords to xtc-trajectory file xtc-precision = 1000 ;== Neighborsearching and short-range nonbonded interactions nstlist = 10; update pairlist ns_type = grid ; pairlist method pbc = xyz ; periodic boundary conditions rlist = 1.3 ; cut-off for neighborsearching - rlist = rvdw+ (0.1 till 0.3) ;== Electrostatics coulombtype = PME rcoulomb= 1.3 ; cut-off for coulomb - rcoulomb = rlist fourierspacing = 0.112 ; nm pme_order = 4 ewald_rtol = 1e-05 optimize_fft= no epsilon_surface = 0 ;== dispersion correction dispcorr= EnerPres ;== Van der Waals vdw-type= shift ; switch rvdw_switch = 0.9 rvdw= 1.0 ; cut-off for vdw ;== OPTIONS FOR WEAK COUPLING ALGORITHMS === Tcoupl = v-rescale; temperature coupling (v-rescale) tc-grps = System ref_t = 298.15 tau_t = 1.0 Pcoupl = berendsen; pressure bath (berendsen) Pcoupltype = isotropic; pressure geometry tau_p = 1.0 ; p-coupoling time compressibility = 4.5e-5 ref_p = 1.01325 ;== GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes ; generate initial velocities gen_temp= 298.15 ; initial temperature gen_seed= -1 ; random seed continuation= no ; since we came from nvt simulation ;== OPTIONS FOR BONDS === constraints = h-bonds constraint_algorithm= lincs shake_tol = 0.1 lincs_order = 4 lincs_warnangle = 30 morse = no lincs_iter = 2 -- 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] Problem with g_dipoles and SPCE water
On 2012-04-10 09:43, Tom Kirchner wrote: Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant (e_sim=109.713) looks very different from experimental (e_exp=78) and reported values for SPCE (e_paper=70). I put the command line and the output below. Did you run the simulation with PME or at the very least RF? Gromacs 4.5.3, SPC/E water, 20ns, NPT, 300K, 1bar g_dipoles -corr total -c dipoles -f md_20ns.xtc -s md_20ns.tpr -b 0 -e 2 You don't need the corr flag for computing the dielectric constant. #== Using 5 as mu_max and -1 as the dipole moment. WARNING: EpsilonRF = 0.0, this really means EpsilonRF = infinity Selected 0: 'System' There are 1024 molecules in the selection Using Volume from topology: 30.2049 nm3 Average volume over run is 30.2103 t0 0, t 2, teller 10001 Dipole moment (Debye) - Average = 2.4883 Std. Dev. = 0.1342 Error = 0. The following averages for the complete trajectory have been calculated: Total M_x = 1.45986 Debye Total M_y = 5.71202 Debye Total M_z = 3.39196 Debye Total M_x2= 10964.8 Debye2 Total M_y2= 10794.4 Debye2 Total M_z2= 10762.4 Debye2 Total |M|^2 = 32521.6 Debye2 Total | M|^2 = 46.2638 Debye2 |M|^2 - | M|^2 = 32475.4 Debye2 Finite system Kirkwood g factor G_k = 5.12208 Infinite system Kirkwood g factor g_k = 3.43028 Epsilon = 109.713 #== I would be really grateful if anybody could point me to my error. I attached my .mdp file in case the error lies there. Best regards Tom -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/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] Problem with g_dipoles and SPCE water
On 2012-04-10 09:57, David van der Spoel wrote: On 2012-04-10 09:43, Tom Kirchner wrote: Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant (e_sim=109.713) looks very different from experimental (e_exp=78) and reported values for SPCE (e_paper=70). I put the command line and the output below. Did you run the simulation with PME or at the very least RF? Gromacs 4.5.3, SPC/E water, 20ns, NPT, 300K, 1bar g_dipoles -corr total -c dipoles -f md_20ns.xtc -s md_20ns.tpr -b 0 -e 2 You don't need the corr flag for computing the dielectric constant. #== Using 5 as mu_max and -1 as the dipole moment. WARNING: EpsilonRF = 0.0, this really means EpsilonRF = infinity Selected 0: 'System' There are 1024 molecules in the selection Using Volume from topology: 30.2049 nm3 Average volume over run is 30.2103 t0 0, t 2, teller 10001 Dipole moment (Debye) - Average = 2.4883 Std. Dev. = 0.1342 Error = 0. Another point: the literature value of the dielectric constant for SPC/E is for the rigid model. Looks like your using a flexible model here. The following averages for the complete trajectory have been calculated: Total M_x = 1.45986 Debye Total M_y = 5.71202 Debye Total M_z = 3.39196 Debye Total M_x2 = 10964.8 Debye2 Total M_y2 = 10794.4 Debye2 Total M_z2 = 10762.4 Debye2 Total |M|^2 = 32521.6 Debye2 Total | M|^2 = 46.2638 Debye2 |M|^2 - | M|^2 = 32475.4 Debye2 Finite system Kirkwood g factor G_k = 5.12208 Infinite system Kirkwood g factor g_k = 3.43028 Epsilon = 109.713 #== I would be really grateful if anybody could point me to my error. I attached my .mdp file in case the error lies there. Best regards Tom -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/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] martini coarse-grained
Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it right? Or should I change SC5 to C-S-C for .gro file? And my definition of tiofen in .itp file it is as followed , Please say me that is it right? ;; TIOFEN [moleculetype] ; molname nrexcl TIO 1 [atoms] ; id type resnr residu atom cgnr charge 1 SC4 1 TIO SI1 1 0 2 SC5 1 TIO SI2 2 0 [constraints] ; i j funct length 1 2 1 0.27 Because I for benzene see a triangle in ngmx program, but for this see a line. Please help me to correction of mistakes. Thank you very much in advance. Best Regards Dina-- 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] Re: Simulation in the high temperature conditions
Justin, Could you tell me for what purposes the definition of the several ref_t values could be usefull? Does this just for measurements of the temperature during simulation for each group separately or is there something else? By the way as I've found in literature another important question about such simulation in high temperature conditions is the selection of the integrator algorithm wich also could enhanse sampling under this conditions. E.g I've found that the BD integrator could be more usefull than leap-frog MD. What timestep and other importnat options defined in mdp should be tken into account within simulation with BD ? I've never perform simulations with this integrator and could not realise how it could enhanse simulation rate in comparison to the MD and what artifacts should expect from that :) James 9 апреля 2012 г. 22:31 пользователь Justin A. Lemkul jalem...@vt.eduнаписал: James Starlight wrote: Mark, Assuming you're raising your temperature during equilibration and then running at high temperature, then you don't want water moving into the receptor interior during equilibration for the same reason you didn't want water moving into the CCl4. And you're going to run further equilibration after taking off all the restraints anyway, right? And if water moves into the receptor interior, then it probably does that under high-temperature equilibrium conditions... It is that I want to prevent movement of water into Ccl4 layer (that is drive by the increased temperature and have not been present in the natural conditions) but allow it to move into the receptor interiour ( that is normally observed experimentally). So the posres application may prevent water to move both into the receptor and Ccl4 so this aproach could not be useful in my case, couldn't it ? No, it wouldn't. I don't understand why you believe some water absolutely can't leak into the CCl4 layer, at least transiently. If you're getting massive mixing, then that's a problem for which I don't know a clear solution in this case. Occasional leakage is not unexpected, as it even occurs in lipid bilayers. True, water and CCl4 are not particularly miscible, but to say that they should remain 100% isolated in reality is not correct. On point, the reference temperature has little to do with whether phases diffuse into (or out of) each other, and lots to do with what ensemble you might be sampling. The actual temperature controls the rate of such diffusion, of course, but if the non-bonded interactions allow for intermixing, then you'll get some degree of that regardless of any other setting. You'd be well advised to check that your CCl4-water boundary behaves acceptably before you invest in the protein simulation... Specifically I've desided to rise temperature of my system to increase conformation sampling of the protein surrounded of the interiour. For this I've devided my system on several parts to couple to separate thermostates. One part is the protein and CCl4 layer wich mimick the membrane and another part is the sorrounded water ( SOL), internal water ( wich may present in the protein interiour transitory but never in the Ccl4 layer) and IONS ( wich are always in the SOL layer). In order that increase the rate of conformation sampling I've gradually increased ref_t of each t_group. In part this result in evaporation of water and some of that water has moved in Ccl4 layer. So its intresting for me might I set ref_t for water_ions group as the specified value ( ref_t= 310 k) and gradually increase only ref_t for the protein_ccl4 group in the annealing manner. As the consequence I want to prevent evaporation of the water but maintain of the overal temperature high of my system tp increase sampling of the protein conformation ? I inderstand that such aproach is very unphysical but aplication of the posres and other tricks are from this theme but works good in some cases :) This sounds really fishy to me. Coupling different parts of a system to thermostats at different temperatures just begs for artifacts. The use of thermostats for separate parts of the system, even at the same temperature, is questionable since you violate energy conservation. Of course, for many cases, they're a necessity and we just go ahead with it ;) If you've got two parts of a system in thermal disequilibrium, then you've got a very odd system with thermostats exchanging different amounts of energy with different portions of the system. I don't know how to predict the effects of such a setup, but I don't recall having seen anything like this done 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
Re: [gmx-users] Problem with g_dipoles and SPCE water
On 04/10/2012 11:10 AM, gmx-users-requ...@gromacs.org wrote: On 2012-04-10 09:57, David van der Spoel wrote: On 2012-04-10 09:43, Tom Kirchner wrote: Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant (e_sim=109.713) looks very different from experimental (e_exp=78) and reported values for SPCE (e_paper=70). I put the command line and the output below. Did you run the simulation with PME or at the very least RF? Gromacs 4.5.3, SPC/E water, 20ns, NPT, 300K, 1bar g_dipoles -corr total -c dipoles -f md_20ns.xtc -s md_20ns.tpr -b 0 -e 2 You don't need the corr flag for computing the dielectric constant. #== Using 5 as mu_max and -1 as the dipole moment. WARNING: EpsilonRF = 0.0, this really means EpsilonRF = infinity Selected 0: 'System' There are 1024 molecules in the selection Using Volume from topology: 30.2049 nm3 Average volume over run is 30.2103 t0 0, t 2, teller 10001 Dipole moment (Debye) - Average = 2.4883 Std. Dev. = 0.1342 Error = 0. Another point: the literature value of the dielectric constant for SPC/E is for the rigid model. Looks like your using a flexible model here. The following averages for the complete trajectory have been calculated: Total M_x = 1.45986 Debye Total M_y = 5.71202 Debye Total M_z = 3.39196 Debye Total M_x2 = 10964.8 Debye2 Total M_y2 = 10794.4 Debye2 Total M_z2 = 10762.4 Debye2 Total |M|^2 = 32521.6 Debye2 Total | M|^2 = 46.2638 Debye2 |M|^2 - | M|^2 = 32475.4 Debye2 Finite system Kirkwood g factor G_k = 5.12208 Infinite system Kirkwood g factor g_k = 3.43028 Epsilon = 109.713 #== I would be really grateful if anybody could point me to my error. I attached my .mdp file in case the error lies there. Best regards Tom -- David van der Spoel, Ph.D., Professor of Biology Thank you for your reply, I used the rigid model. I also used PME, I think this is the error, for g_dipoles seems to be constructed for reaction field. Is this correct? I'll redo the simulation with reaction field now. Best Tom Kirchner -- 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] Problem with g_dipoles and SPCE water
On 2012-04-10 11:16, Tom Kirchner wrote: On 04/10/2012 11:10 AM, gmx-users-requ...@gromacs.org wrote: On 2012-04-10 09:57, David van der Spoel wrote: On 2012-04-10 09:43, Tom Kirchner wrote: Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant (e_sim=109.713) looks very different from experimental (e_exp=78) and reported values for SPCE (e_paper=70). I put the command line and the output below. Did you run the simulation with PME or at the very least RF? Gromacs 4.5.3, SPC/E water, 20ns, NPT, 300K, 1bar g_dipoles -corr total -c dipoles -f md_20ns.xtc -s md_20ns.tpr -b 0 -e 2 You don't need the corr flag for computing the dielectric constant. #== Using 5 as mu_max and -1 as the dipole moment. WARNING: EpsilonRF = 0.0, this really means EpsilonRF = infinity Selected 0: 'System' There are 1024 molecules in the selection Using Volume from topology: 30.2049 nm3 Average volume over run is 30.2103 t0 0, t 2, teller 10001 Dipole moment (Debye) - Average = 2.4883 Std. Dev. = 0.1342 Error = 0. Another point: the literature value of the dielectric constant for SPC/E is for the rigid model. Looks like your using a flexible model here. The following averages for the complete trajectory have been calculated: Total M_x = 1.45986 Debye Total M_y = 5.71202 Debye Total M_z = 3.39196 Debye Total M_x2 = 10964.8 Debye2 Total M_y2 = 10794.4 Debye2 Total M_z2 = 10762.4 Debye2 Total |M|^2 = 32521.6 Debye2 Total | M|^2 = 46.2638 Debye2 |M|^2 - | M|^2 = 32475.4 Debye2 Finite system Kirkwood g factor G_k = 5.12208 Infinite system Kirkwood g factor g_k = 3.43028 Epsilon = 109.713 #== I would be really grateful if anybody could point me to my error. I attached my .mdp file in case the error lies there. Best regards Tom -- David van der Spoel, Ph.D., Professor of Biology Thank you for your reply, I used the rigid model. I also used PME, I think this is the error, for g_dipoles seems to be constructed for reaction field. Is this correct? I'll redo the simulation with reaction field now. Best Tom Kirchner No! g_dipoles does not care. You may have a remnant command in your mdp file (-DFLEXIBLE), please remove it. For rigid model there should not be any fluctations in the dipole. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/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] Error: 4095 characters, fgets2 has size 4095
Dear Gmx Users, It is 1st time I came across such problem. While preparing my NPT simulation before umbrella samping: grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' Its not about the files in bad format as I have never had this problem - I am using Gromacs 4.5.4 installed on the cluster, I am using PuTTy shell. I always use dos2gmx ibefore processing. Can you advise? Steven -- 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] Error: 4095 characters, fgets2 has size 4095
Hi Steven, you might have to remove files with weird names (such as ._name) in the directory where you run grompp or in your forcefield directory. Carsten On Apr 10, 2012, at 11:52 AM, Steven Neumann wrote: Dear Gmx Users, It is 1st time I came across such problem. While preparing my NPT simulation before umbrella samping: grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' Its not about the files in bad format as I have never had this problem - I am using Gromacs 4.5.4 installed on the cluster, I am using PuTTy shell. I always use dos2gmx ibefore processing. Can you advise? Steven -- 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] Error: 4095 characters, fgets2 has size 4095
Thank you for the reply. I do not have such files in my directory or in my force field. On Tue, Apr 10, 2012 at 10:59 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Steven, you might have to remove files with weird names (such as ._name) in the directory where you run grompp or in your forcefield directory. Carsten On Apr 10, 2012, at 11:52 AM, Steven Neumann wrote: Dear Gmx Users, It is 1st time I came across such problem. While preparing my NPT simulation before umbrella samping: grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' Its not about the files in bad format as I have never had this problem - I am using Gromacs 4.5.4 installed on the cluster, I am using PuTTy shell. I always use dos2gmx ibefore processing. Can you advise? Steven -- 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] Gromacs on HPC workstations ?
Hi, I'm currently looking for hardware solutions to run MDs and would like to benefit from your experience concerning the hardware. It would mainly be simulations in the range of several thousands of CPU hours, and occasionally for hundreds of K hours (paralleled on 64 to 256 nodes max). There's a link of Erik Lindahl's Building Clusters on gromacs website, but it's now 5 years old and the balance between pros and cons of having a rack vs a workstations might have considerately changed (thinking about 16-core interlagos chips allowing to have 64-cores on a single workstation). Also, with the increasing availability of HPC cloud computing resources, choosing between an inhouse cluster and the cloud solution can be difficult. So any advice concerning the use of HPC workstations (stability, performance, cost compared to clusters) or commercial cloud solutions would be greatly appreciated ! Thanks in advance, Jonathan. -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-on-HPC-workstations-tp4735461p4735461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Error: 4095 characters, fgets2 has size 4095
On 2012-04-10 12:02, Steven Neumann wrote: Thank you for the reply. I do not have such files in my directory or in my force field. did you mean dos2unix? try: wc grompp.mdp to count the number of lines. There should be may. In fact grompp probably tells you which input file is erroneous, doesn't it? On Tue, Apr 10, 2012 at 10:59 AM, Carsten Kutzner ckut...@gwdg.de mailto:ckut...@gwdg.de wrote: Hi Steven, you might have to remove files with weird names (such as ._name) in the directory where you run grompp or in your forcefield directory. Carsten On Apr 10, 2012, at 11:52 AM, Steven Neumann wrote: Dear Gmx Users, It is 1st time I came across such problem. While preparing my NPT simulation before umbrella samping: grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095. The line starts with: '20s' Its not about the files in bad format as I have never had this problem - I am using Gromacs 4.5.4 installed on the cluster, I am using PuTTy shell. I always use dos2gmx ibefore processing. Can you advise? Steven -- gmx-users mailing list gmx-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/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-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/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://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/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] Error: 4095 characters, fgets2 has size 4095
On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2012-04-10 12:02, Steven Neumann wrote: Thank you for the reply. I do not have such files in my directory or in my force field. did you mean dos2unix? try: wc grompp.mdp to count the number of lines. There should be may. In fact grompp probably tells you which input file is erroneous, doesn't it? It does not provide the information which file is this. I checked every file with wc -L and it does not exceed 100. However I read that creating gurgle.dat - empty file may solve it. When I did it and process grmpp: Ignoring obsolete mdp entry 'title' Generated 67161 of the 67161 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 49536 of the 67161 1-4 parameter combinations WARNING: File is empty *** glibc detected *** grompp: double free or corruption (!prev): 0x01cf0480 *** === Backtrace: = /lib64/libc.so.6[0x30fc675296] /lib64/libc.so.6(fclose+0x14d)[0x30fc665a1d] grompp[0x5a5952] grompp[0x59ba29] grompp[0x5a67bd] grompp[0x5a661f] grompp[0x5cb798] grompp[0x5a7184] grompp[0x41fd8c] grompp[0x41fa38] grompp[0x408a8d] grompp[0x405422] /lib64/libc.so.6(__libc_start_main+0xfd)[0x30fc61ecdd] grompp[0x404eaa] === Memory map: 0040-00756000 r-xp 00:1f 107224920 /apps/gromacs/4.5.4/bin/grompp 00855000-00865000 rwxp 00355000 00:1f 107224920 /apps/gromacs/4.5.4/bin/grompp 00865000-00894000 rwxp 00:00 0 01cde000-020a3000 rwxp 00:00 0 [heap] 30fbe0-30fbe2 r-xp 08:01 558856 /lib64/ld-2.12.so 30fc01f000-30fc02 r-xp 0001f000 08:01 558856 /lib64/ld-2.12.so 30fc02-30fc021000 rwxp 0002 08:01 558856 /lib64/ld-2.12.so 30fc021000-30fc022000 rwxp 00:00 0 30fc20-30fc202000 r-xp 08:01 554053 /lib64/libdl-2.12.so 30fc202000-30fc402000 ---p 2000 08:01 554053 /lib64/libdl-2.12.so 30fc402000-30fc403000 r-xp 2000 08:01 554053 /lib64/libdl-2.12.so 30fc403000-30fc404000 rwxp 3000 08:01 554053 /lib64/libdl-2.12.so 30fc60-30fc786000 r-xp 08:01 558857 /lib64/libc-2.12.so 30fc786000-30fc986000 ---p 00186000 08:01 558857 /lib64/libc-2.12.so 30fc986000-30fc98a000 r-xp 00186000 08:01 558857 /lib64/libc-2.12.so 30fc98a000-30fc98b000 rwxp 0018a000 08:01 558857 /lib64/libc-2.12.so 30fc98b000-30fc99 rwxp 00:00 0 30fca0-30fca17000 r-xp 08:01 558858 /lib64/libpthread-2.12.so 30fca17000-30fcc16000 ---p 00017000 08:01 558858 /lib64/libpthread-2.12.so 30fcc16000-30fcc17000 r-xp 00016000 08:01 558858 /lib64/libpthread-2.12.so 30fcc17000-30fcc18000 rwxp 00017000 08:01 558858 /lib64/libpthread-2.12.so 30fcc18000-30fcc1c000 rwxp 00:00 0 30fce0-30fce83000 r-xp 08:01 558867 /lib64/libm-2.12.so 30fce83000-30fd082000 ---p 00083000 08:01 558867 /lib64/libm-2.12.so 30fd082000-30fd083000 r-xp 00082000 08:01 558867 /lib64/libm-2.12.so 30fd083000-30fd084000 rwxp 00083000 08:01 558867 /lib64/libm-2.12.so 30fd20-30fd215000 r-xp 08:01 558866 /lib64/libz.so.1.2.3 30fd215000-30fd414000 ---p 00015000 08:01 558866 /lib64/libz.so.1.2.3 30fd414000-30fd415000 r-xp 00014000 08:01 558866 /lib64/libz.so.1.2.3 30fd415000-30fd416000 rwxp 00015000 08:01 558866 /lib64/libz.so.1.2.3 30fd60-30fd607000 r-xp 08:01 558859 /lib64/librt-2.12.so 30fd607000-30fd806000 ---p 7000 08:01 558859 /lib64/librt-2.12.so 30fd806000-30fd807000 r-xp 6000 08:01 558859 /lib64/librt-2.12.so 30fd807000-30fd808000 rwxp 7000 08:01 558859 /lib64/librt-2.12.so 30fe60-30fe616000 r-xp 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 30fe616000-30fe815000 ---p 00016000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 30fe815000-30fe816000 rwxp 00015000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 310620-3106347000 r-xp 08:01 738508 /usr/lib64/libxml2.so.2.7.6 3106347000-3106546000 ---p 00147000 08:01 738508 /usr/lib64/libxml2.so.2.7.6 3106546000-310655 rwxp 00146000 08:01 738508 /usr/lib64/libxml2.so.2.7.6 310655-3106551000 rwxp 00:00 0 310d60-310d616000 r-xp 08:01 558894 /lib64/libnsl-2.12.so 310d616000-310d815000 ---p 00016000 08:01 558894 /lib64/libnsl-2.12.so 310d815000-310d816000 r-xp 00015000 08:01 558894 /lib64/libnsl-2.12.so 310d816000-310d817000 rwxp 00016000 08:01 558894 /lib64/libnsl-2.12.so 310d817000-310d819000 rwxp 00:00 0 2b3cd1d8b000-2b3cd1d9e000 rwxp 00:00 0 2b3cd1dad000-2b3cd1dae000 rwxp 00:00 0 2b3cd1dae000-2b3cd202 r-xp 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so 2b3cd202-2b3cd211f000 ---p 00272000 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so 2b3cd211f000-2b3cd2124000 rwxp 00271000 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so 2b3cd2124000-2b3cd2125000 rwxp 00:00 0 2b3cd2125000-2b3cd230a000 r-xp 00:1f 92286570 /apps/intel/ict/mpi/3.1.038/lib64/libmpi.so.3.2 2b3cd230a000-2b3cd240a000 ---p 001e5000 00:1f
Re: [gmx-users] SS bond forcing
pitheve...@free.fr wrote: Here is what I have done: First, I created the .gro file with the command line: pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing Then, I added at the end of my test.top file the following lines (I double checked the atom numbers): [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 37 140 1 0 1 0.19 0.21 0.22 1 then, I done: editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0 and finally get my new pdb file with: editconf -f test-min.gro -o test-min.pdb But it didn't seemed it had make the two sufur atom closer than if I didn't add the distance_restrain in the top file. Did I do something wrong? Simple energy minimization is unlikely to give rise to the structural changes you need to bring these atoms close together. Running a short MD simulation may work, though if the atoms are very far apart and you force them together quickly, you may have stability issues. -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/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] Error: 4095 characters, fgets2 has size 4095
On 2012-04-10 12:38, Steven Neumann wrote: On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: On 2012-04-10 12:02, Steven Neumann wrote: Thank you for the reply. I do not have such files in my directory or in my force field. did you mean dos2unix? try: wc grompp.mdp to count the number of lines. There should be may. In fact grompp probably tells you which input file is erroneous, doesn't it? It does not provide the information which file is this. I checked every file with wc -L and it does not exceed 100. However I read that creating gurgle.dat - empty file may solve it. When I did it and process grmpp: weird. On what kind of machine are you running? Did you do source PATHTOGROMACS/bin/GMXRC ? Ignoring obsolete mdp entry 'title' Generated 67161 of the 67161 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 49536 of the 67161 1-4 parameter combinations WARNING: File is empty *** glibc detected *** grompp: double free or corruption (!prev): 0x01cf0480 *** === Backtrace: = /lib64/libc.so.6[0x30fc675296] /lib64/libc.so.6(fclose+0x14d)[0x30fc665a1d] grompp[0x5a5952] grompp[0x59ba29] grompp[0x5a67bd] grompp[0x5a661f] grompp[0x5cb798] grompp[0x5a7184] grompp[0x41fd8c] grompp[0x41fa38] grompp[0x408a8d] grompp[0x405422] /lib64/libc.so.6(__libc_start_main+0xfd)[0x30fc61ecdd] grompp[0x404eaa] === Memory map: 0040-00756000 r-xp 00:1f 107224920 /apps/gromacs/4.5.4/bin/grompp 00855000-00865000 rwxp 00355000 00:1f 107224920 /apps/gromacs/4.5.4/bin/grompp 00865000-00894000 rwxp 00:00 0 01cde000-020a3000 rwxp 00:00 0 [heap] 30fbe0-30fbe2 r-xp 08:01 558856 /lib64/ld-2.12.so http://ld-2.12.so 30fc01f000-30fc02 r-xp 0001f000 08:01 558856 /lib64/ld-2.12.so http://ld-2.12.so 30fc02-30fc021000 rwxp 0002 08:01 558856 /lib64/ld-2.12.so http://ld-2.12.so 30fc021000-30fc022000 rwxp 00:00 0 30fc20-30fc202000 r-xp 08:01 554053 /lib64/libdl-2.12.so http://libdl-2.12.so 30fc202000-30fc402000 ---p 2000 08:01 554053 /lib64/libdl-2.12.so http://libdl-2.12.so 30fc402000-30fc403000 r-xp 2000 08:01 554053 /lib64/libdl-2.12.so http://libdl-2.12.so 30fc403000-30fc404000 rwxp 3000 08:01 554053 /lib64/libdl-2.12.so http://libdl-2.12.so 30fc60-30fc786000 r-xp 08:01 558857 /lib64/libc-2.12.so http://libc-2.12.so 30fc786000-30fc986000 ---p 00186000 08:01 558857 /lib64/libc-2.12.so http://libc-2.12.so 30fc986000-30fc98a000 r-xp 00186000 08:01 558857 /lib64/libc-2.12.so http://libc-2.12.so 30fc98a000-30fc98b000 rwxp 0018a000 08:01 558857 /lib64/libc-2.12.so http://libc-2.12.so 30fc98b000-30fc99 rwxp 00:00 0 30fca0-30fca17000 r-xp 08:01 558858 /lib64/libpthread-2.12.so http://libpthread-2.12.so 30fca17000-30fcc16000 ---p 00017000 08:01 558858 /lib64/libpthread-2.12.so http://libpthread-2.12.so 30fcc16000-30fcc17000 r-xp 00016000 08:01 558858 /lib64/libpthread-2.12.so http://libpthread-2.12.so 30fcc17000-30fcc18000 rwxp 00017000 08:01 558858 /lib64/libpthread-2.12.so http://libpthread-2.12.so 30fcc18000-30fcc1c000 rwxp 00:00 0 30fce0-30fce83000 r-xp 08:01 558867 /lib64/libm-2.12.so http://libm-2.12.so 30fce83000-30fd082000 ---p 00083000 08:01 558867 /lib64/libm-2.12.so http://libm-2.12.so 30fd082000-30fd083000 r-xp 00082000 08:01 558867 /lib64/libm-2.12.so http://libm-2.12.so 30fd083000-30fd084000 rwxp 00083000 08:01 558867 /lib64/libm-2.12.so http://libm-2.12.so 30fd20-30fd215000 r-xp 08:01 558866 /lib64/libz.so.1.2.3 30fd215000-30fd414000 ---p 00015000 08:01 558866 /lib64/libz.so.1.2.3 30fd414000-30fd415000 r-xp 00014000 08:01 558866 /lib64/libz.so.1.2.3 30fd415000-30fd416000 rwxp 00015000 08:01 558866 /lib64/libz.so.1.2.3 30fd60-30fd607000 r-xp 08:01 558859 /lib64/librt-2.12.so http://librt-2.12.so 30fd607000-30fd806000 ---p 7000 08:01 558859 /lib64/librt-2.12.so http://librt-2.12.so 30fd806000-30fd807000 r-xp 6000 08:01 558859 /lib64/librt-2.12.so http://librt-2.12.so 30fd807000-30fd808000 rwxp 7000 08:01 558859 /lib64/librt-2.12.so http://librt-2.12.so 30fe60-30fe616000 r-xp 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 30fe616000-30fe815000 ---p 00016000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 30fe815000-30fe816000 rwxp 00015000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 310620-3106347000 r-xp 08:01 738508 /usr/lib64/libxml2.so.2.7.6 3106347000-3106546000 ---p 00147000 08:01 738508 /usr/lib64/libxml2.so.2.7.6 3106546000-310655 rwxp 00146000 08:01 738508 /usr/lib64/libxml2.so.2.7.6 310655-3106551000 rwxp 00:00 0 310d60-310d616000 r-xp 08:01 558894 /lib64/libnsl-2.12.so http://libnsl-2.12.so 310d616000-310d815000 ---p 00016000 08:01 558894 /lib64/libnsl-2.12.so http://libnsl-2.12.so
Re: [gmx-users] How to extract the first three PC's cosine content from the coscont.xvg file?
Hi Catherine, A converged system will yield low cosine content. But that can't be turned around! I can think of a lot of lines that don't match well with a cosine, but that are inconsistent with convergence. That said, the index in the .xvg file is the principal component index. So the projection on the first pc has a cosine content of 0.6. Cheers, Tsjerk On Tue, Apr 10, 2012 at 5:28 AM, a a pat...@hotmail.com wrote: Dear Sir/Madam, I used the following steps to get the cosine content for my trajectories, could you please kindly tell me how to interpret the results? /usr/local/gromacs/bin/g_covar_d -s ../test.pdb -f test.binpos -o -v /usr/local/gromacs/bin/g_anaeig_d -s ../test.pdb -f test.binpos -v eigenvec.trr -proj /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8 In the final coscont.xvg, I found the followings: # This file was created Tue Apr 10 10:59:12 2012 # by the following command: # /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8 # # g_analyze_d is p art of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @ title Cosine content @ xaxis label set / half periods @ yaxis label cosine content @TYPE xy 1 0.602921 2 0.011185 3 0.0659901 4 0.425943 5 0.204306 6 0.439315 7 0.0288551 8 0.0830944 I read some literature quoted the first three PCs's cosine content, if the cosine content close to zero, the trajectory is converged. How can I extract the first three PCs's cosine content from the above conscont.xvg file? Please kindly help. Best regards, Catherine -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Re: Simulation in the high temperature conditions
James Starlight wrote: Justin, Could you tell me for what purposes the definition of the several ref_t values could be usefull? Does this just for measurements of the temperature during simulation for each group separately or is there something else? Each ref_t value is the target temperature for however many groups you have assigned to separate thermostats. By the way as I've found in literature another important question about such simulation in high temperature conditions is the selection of the integrator algorithm wich also could enhanse sampling under this conditions. E.g I've found that the BD integrator could be more usefull than leap-frog MD. What timestep and other importnat options defined in mdp should be tken into account within simulation with BD ? I've never perform simulations with this integrator and could not realise how it could enhanse simulation rate in comparison to the MD and what artifacts should expect from that :) I have never used the bd integrator so I cannot offer any help here. I don't see any magical reason why you should expect it to enhance sampling though. -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/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] martini coarse-grained
Where did you find the topology? On Apr 10, 2012, at 10:44 AM, dina dusti wrote: Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C- C. Is it right? Or should I change SC5 to C-S-C for .gro file? And my definition of tiofen in .itp file it is as followed , Please say me that is it right? ;; TIOFEN [moleculetype] ; molname nrexcl TIO 1 [atoms] ; idtyperesnr residu atomcgnrcharge 1 SC4 1 TIO SI1 1 0 2 SC5 1 TIO SI22 0 [constraints] ; i j funct length 1 2 1 0.27 Because I for benzene see a triangle in ngmx program, but for this see a line. Please help me to correction of mistakes. Thank you very much in advance. Best Regards Dina -- 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] SS bond forcing
How long the MD simulation should be? The problem is that I run multiple simulation (a hundred at a time) and the MD are really time consuming. I should probably can't do it, if the time you propose is too long, I probably forget it. Thank you -- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole Doctorale B3MI Université Paris Diderot - Paris 7 2012/4/10 Justin A. Lemkul jalem...@vt.edu pitheve...@free.fr wrote: Here is what I have done: First, I created the .gro file with the command line: pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing Then, I added at the end of my test.top file the following lines (I double checked the atom numbers): [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 37 140 1 0 1 0.19 0.21 0.22 1 then, I done: editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0 and finally get my new pdb file with: editconf -f test-min.gro -o test-min.pdb But it didn't seemed it had make the two sufur atom closer than if I didn't add the distance_restrain in the top file. Did I do something wrong? Simple energy minimization is unlikely to give rise to the structural changes you need to bring these atoms close together. Running a short MD simulation may work, though if the atoms are very far apart and you force them together quickly, you may have stability issues. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] SS bond forcing
Pierre THEVENET wrote: How long the MD simulation should be? The problem is that I run multiple simulation (a hundred at a time) and the MD are really time consuming. I should probably can't do it, if the time you propose is too long, I probably forget it. I can't predict how much time it would take. How far apart are the S atoms from one another? If it's just a small distance beyond the normal cutoff, it should be quick, a few hundred ps or less (assuming everything else is otherwise stable). If the distance is very long and would require large structural transitions to accommodate, then you're probably in trouble. -Justin Thank you -- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole Doctorale B3MI Université Paris Diderot - Paris 7 2012/4/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu pitheve...@free.fr mailto:pitheve...@free.fr wrote: Here is what I have done: First, I created the .gro file with the command line: pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing Then, I added at the end of my test.top file the following lines (I double checked the atom numbers): [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 37 140 1 0 1 0.19 0.21 0.22 1 then, I done: editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0 and finally get my new pdb file with: editconf -f test-min.gro -o test-min.pdb But it didn't seemed it had make the two sufur atom closer than if I didn't add the distance_restrain in the top file. Did I do something wrong? Simple energy minimization is unlikely to give rise to the structural changes you need to bring these atoms close together. Running a short MD simulation may work, though if the atoms are very far apart and you force them together quickly, you may have stability issues. -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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- 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/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] Re: Simulation in the high temperature conditions
Justin, 10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul jalem...@vt.eduнаписал: I have never used the bd integrator so I cannot offer any help here. I don't see any magical reason why you should expect it to enhance sampling though. I've found in the literature that this integrator could rise the integration-time-step from common 1-2fs used with the MD-integrator. By the way I've tried to test my system equilibrated in the hight temperature in different conditions. As the consequence when I've removed all posres ( on the last stage of equilibration it's value was 200 for backbone atoms only) from my protein the alpha helixes have been destabilised already after 3ns of such unconstrained simulation ( ref_t= 700k). So I suppose that the presence of the some constrained factor is needed to prevent destabilisation but allow conformation sampling. I see three alternative ways of my production MD run with enhanced sampling. 1- First of all as the most trivial way I'm thinking of using soft posres applied on backbone atoms only with the constained value ( 50-100 kj*nm2) corresponded to the energy of the thermal motion. 2- Also I've thought about application of the harmonic distance_restraince (instead of posres) on the all backbone atoms exept of flexible loops where this disres must be in the longer range ( e.g up to 15-20A) but I could not realise about usefullness of such aproach because I cant define value for such disres for the atoms in helixes. It's known that conformation transitions wich I want to ssample accompanied by the large scale motions in the helical segments ( up to 10-15 A). At the same time such big fluctuations on the other atoms may destabiise regions wich are more rigid. Should I define several sets of restrains for my protein to allow one regions move with bigger amplitudes in comparison with rigid fragments ? 3- Finally alternative aproach is the ussage of common temperature ( ref_t=310k) in the production run but using starting velocities obtained from the nvt equilibrration obtained with the hight ( 700k) temperature. Can I enhance sampling using that starting conditions ? What from this three strategies is the most suitable? IS there any alternative ways for such high-temperature simulation ? Thanks for help again, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] on 2 different mini.mdp file
Dear All, The first mini.mdp is as following: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) The second mini.mdp is as folowing: ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.4 ; Short-range electrostatic cut-off rvdw= 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions The difference is the cut-off. One is 1.4,the other is 1.0. Can anyone explain their difference on the influence of the MD result? Suppose I use AMBER 99SB force field, will you lease tell me how can decide the value of the above cut-offs? Cheers, Acoot-- 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] SS bond forcing
In most cases (it is form predicted structures) if the bonds is not formes, the S atoms are at the opposite side of the backbone. And I work on peptides, so the length of the structure isn't that big (50 residues max) -- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole Doctorale B3MI Université Paris Diderot - Paris 7 2012/4/10 Justin A. Lemkul jalem...@vt.edu Pierre THEVENET wrote: How long the MD simulation should be? The problem is that I run multiple simulation (a hundred at a time) and the MD are really time consuming. I should probably can't do it, if the time you propose is too long, I probably forget it. I can't predict how much time it would take. How far apart are the S atoms from one another? If it's just a small distance beyond the normal cutoff, it should be quick, a few hundred ps or less (assuming everything else is otherwise stable). If the distance is very long and would require large structural transitions to accommodate, then you're probably in trouble. -Justin Thank you -- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole Doctorale B3MI Université Paris Diderot - Paris 7 2012/4/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu pitheve...@free.fr mailto:pitheve...@free.fr wrote: Here is what I have done: First, I created the .gro file with the command line: pdb2gmx -f test.pdb -o test.gro -p test.top -ignh -missing Then, I added at the end of my test.top file the following lines (I double checked the atom numbers): [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 37 140 1 0 1 0.19 0.21 0.22 1 then, I done: editconf -f test.gro -o test-box.gro -d 2.0 -c -bt cubic grompp -c test-box.gro -p test.top -o test-min.tpr -f test-em.mdp mdrun -s test-min.tpr -c test-min.gro -deffnm test-min -v -nice 0 and finally get my new pdb file with: editconf -f test-min.gro -o test-min.pdb But it didn't seemed it had make the two sufur atom closer than if I didn't add the distance_restrain in the top file. Did I do something wrong? Simple energy minimization is unlikely to give rise to the structural changes you need to bring these atoms close together. Running a short MD simulation may work, though if the atoms are very far apart and you force them together quickly, you may have stability issues. -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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-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. 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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?
[gmx-users] lipid.itp for AMBER-GAFF
Hello, I am following the 'KALP15 in DPPC tutorial' but using GAFF with DOPC (from http://lipidbook.bioch.ox.ac.uk/package/show/id/32.html) and my membrane protein. Is there an equivalent file to lipid.itp for AMBER-GAFF? Kind regards, Henry Henry Hocking, PhD Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 CH Utrecht, The Netherlands Phone: +31-30-2532875 Fax: +31-30-253 7623 E-mail: h.g.hock...@uu.nl -- 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] Can gromacs handle reflective boundary condition ?
Dear, Can gromacs handle reflective boundary condition, in order to remove the periodicity of Z-axis ? Do I need to take advantage of walls and Ewald ? Thanks so much! Yours, John Yu 2012.04.10-- 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] lipid.itp for AMBER-GAFF
Henry Hocking wrote: Hello, I am following the 'KALP15 in DPPC tutorial' but using GAFF with DOPC (from http://lipidbook.bioch.ox.ac.uk/package/show/id/32.html) and my membrane protein. Is there an equivalent file to lipid.itp for AMBER-GAFF? There is a lipid force field that has been contributed (last item in the list): http://www.gromacs.org/Downloads/User_contributions/Force_fields I've never used it, but there is a reference that should indicate if it is worthwhile for you. -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/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] Structures and topologies of cholesterol-containing membranes
Hi, we have recently put a website online with structures and topologies of a large set of 28 different cholesterol-containing membranes: http://cmb.bio.uni-goettingen.de/cholmembranes.html Structures of membranes containing - DMPC - DPPC - POPC - DOPC - POPE - POPE and POPC plus different amounts of cholesterol are available. Please feel free to use them if they are relevant for your research (we only ask to cite our papers). Happy simulating, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- 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] SS bond forcing
Pierre THEVENET wrote: In most cases (it is form predicted structures) if the bonds is not formes, the S atoms are at the opposite side of the backbone. And I work on peptides, so the length of the structure isn't that big (50 residues max) Well, if you try the distance restraint approach, I'd do it in the absence of any solvent since there likely will be rather large structural changes (and thus very fast protein-solvent clashes as the restraints are satisfied), unless the peptide is pretty compact. Really short MD should tell you if this will even be feasible. -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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] on 2 different mini.mdp file
Acoot Brett wrote: Dear All, The first mini.mdp is as following: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) The second mini.mdp is as folowing: ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.4 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.4 ; Short-range electrostatic cut-off rvdw= 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions The difference is the cut-off. One is 1.4,the other is 1.0. Can anyone explain their difference on the influence of the MD result? You should be able to see this yourself from the resulting structure and energetic terms. I'd suspect for simple energy minimization (which, by definition, is not MD) the differences will be rather small. An actual MD simulation, however, may be influenced significantly. Suppose I use AMBER 99SB force field, will you lease tell me how can decide the value of the above cut-offs? By reading the primary reference for the force field to understand the conditions for which it was parameterized, then any subsequent tests of the force field that may have discovered improvements. Researching a force field and its proper implementation can often be the most time-consuming part of preparing your simulations, but it's better to spend a few days reading and searching than a few weeks or months generating junk data because your setup is wrong ;) -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/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] Re: Simulation in the high temperature conditions
James Starlight wrote: Justin, 10 апреля 2012 г. 16:21 пользователь Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu написал: I have never used the bd integrator so I cannot offer any help here. I don't see any magical reason why you should expect it to enhance sampling though. I've found in the literature that this integrator could rise the integration-time-step from common 1-2fs used with the MD-integrator. The timestep is not directly tied to the integrator. The timestep is decided based on the fastest motions in the system. Using constraints for bonds allows an increase in timestep. There is information about these factors in the Gromacs manual, and likely any textbook regarding MD simulation. A 2-fs timestep with the 'md' (leap-frog) integrator when using constraints is quite common. By the way I've tried to test my system equilibrated in the hight temperature in different conditions. As the consequence when I've removed all posres ( on the last stage of equilibration it's value was 200 for backbone atoms only) from my protein the alpha helixes have been destabilised already after 3ns of such unconstrained simulation ( ref_t= 700k). That's not surprising. Most force fields were not designed to reproduce the structure of proteins at ambient temperature when exposed to conditions that exceed boiling. Denaturation at this temperature should be expected. So I suppose that the presence of the some constrained factor is needed to prevent destabilisation but allow conformation sampling. I see three alternative ways of my production MD run with enhanced sampling. 1- First of all as the most trivial way I'm thinking of using soft posres applied on backbone atoms only with the constained value ( 50-100 kj*nm2) corresponded to the energy of the thermal motion. 2- Also I've thought about application of the harmonic distance_restraince (instead of posres) on the all backbone atoms exept of flexible loops where this disres must be in the longer range ( e.g up to 15-20A) but I could not realise about usefullness of such aproach because I cant define value for such disres for the atoms in helixes. Sure you can. Use genrestr with a suitable index group. The use of lots of distance restraints precludes the use of DD, so you're limited to using mdrun -pd, which is a lot slower and may counteract any perceived benefit in terms of simulation time. It's known that conformation transitions wich I want to ssample accompanied by the large scale motions in the helical segments ( up to 10-15 A). At the same time such big fluctuations on the other atoms may destabiise regions wich are more rigid. Should I define several sets of restrains for my protein to allow one regions move with bigger amplitudes in comparison with rigid fragments ? All of this sounds like a large bias on your results and deconvoluting what is real versus what you've caused to happen will be a huge headache. 3- Finally alternative aproach is the ussage of common temperature ( ref_t=310k) in the production run but using starting velocities obtained from the nvt equilibrration obtained with the hight ( 700k) temperature. Can I enhance sampling using that starting conditions ? I don't think so. We've discussed this already. I suspect your thermostat will have a hard time converging and all you've ended up doing is creating a weird, undefined ensemble to start your simulations. What from this three strategies is the most suitable? IS there any alternative ways for such high-temperature simulation ? High-temperature MD is not a new concept. There's lots of literature about it. But if you find yourself having to engineer fancy ways of simply keeping your protein stable, it starts getting too fishy to be plausible, IMHO. -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/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] SS bond forcing
Ok. Thank you for your help. I will try to do it and see if it not too time consuming. -- Pierre THEVENET Ph.D. Candidate INSERM - MTi Ecole Doctorale B3MI Université Paris Diderot - Paris 7 2012/4/10 Justin A. Lemkul jalem...@vt.edu Pierre THEVENET wrote: In most cases (it is form predicted structures) if the bonds is not formes, the S atoms are at the opposite side of the backbone. And I work on peptides, so the length of the structure isn't that big (50 residues max) Well, if you try the distance restraint approach, I'd do it in the absence of any solvent since there likely will be rather large structural changes (and thus very fast protein-solvent clashes as the restraints are satisfied), unless the peptide is pretty compact. Really short MD should tell you if this will even be feasible. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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] protein folding / pbc
Hi All, I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure. I set up pbc with the starting structure which is compact. When defining the box we use editconf and set up the -d 1.0 as the distance from the protein to the box edge. It is said that a protein should never see its periodic image. If during the simulation the protein starts unfolding, the minimum distance from the protein to the box edge will no longer be 1.0 nm. And it is possible that the length of the protein is even longer than the box dimension and the protein may see its periodic image in the neighbored box. Is this going to be a problem? I am also confused that it is also said that (parts of) the molecule(s) diffuse out of the box is not a problem. Is this conflicted with a protein should never see its periodic image? Thank you. Best, Huilin -- 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] protein folding / pbc
On 11/04/2012 1:24 AM, Shi, Huilin wrote: Hi All, I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure. I set up pbc with the starting structure which is compact. When defining the box we use editconf and set up the -d 1.0 as the distance from the protein to the box edge. It is said that a protein should never see its periodic image. If during the simulation the protein starts unfolding, the minimum distance from the protein to the box edge will no longer be 1.0 nm. And it is possible that the length of the protein is even longer than the box dimension and the protein may see its periodic image in the neighbored box. Is this going to be a problem? Yes, if you don't allow for it from the start. Some test simulations with implicit solvent are probably priceless here. I am also confused that it is also said that (parts of) the molecule(s) diffuse out of the box is not a problem. Is this conflicted with a protein should never see its periodic image? Sometimes - can depend on orientation of molecule wrt box. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] multiple dihedral function types - regd
Dear gromacs users, For one of my residues i have two types of dihedral functions, i.e C-C dihedrals are in periodic type and C-O dihedrals are in the Ryckaert-bellemans type, now i want to generate the topology file for this residue is it possible to use the two dihedral function types for this residue. I have tried by using two different dihedraltypes directives one is for the periodic type and another one is for Ryckaert-Bellemans function, but how can i incorporate the two functional types in the dihedrals section of the bondedtypes directive in aminoacids.rtp. or is there any methods in gromacs to convert one dihedral functional form to the other. Thank you, Regards, Ramesh. -- 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] protein folding / pbc
So if I wanna run a simulation to unfold the protein, I need make a big box that is large enough so that the unfolded protein is still smaller than the box in any dimension. Is this correct? Thanks. Huilin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Tuesday, April 10, 2012 11:54 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] protein folding / pbc On 11/04/2012 1:24 AM, Shi, Huilin wrote: Hi All, I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure. I set up pbc with the starting structure which is compact. When defining the box we use editconf and set up the -d 1.0 as the distance from the protein to the box edge. It is said that a protein should never see its periodic image. If during the simulation the protein starts unfolding, the minimum distance from the protein to the box edge will no longer be 1.0 nm. And it is possible that the length of the protein is even longer than the box dimension and the protein may see its periodic image in the neighbored box. Is this going to be a problem? Yes, if you don't allow for it from the start. Some test simulations with implicit solvent are probably priceless here. I am also confused that it is also said that (parts of) the molecule(s) diffuse out of the box is not a problem. Is this conflicted with a protein should never see its periodic image? Sometimes - can depend on orientation of molecule wrt box. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box generation for monoclinic crystal - regd
Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 125.4 90 it gave the following warning WARNING: Triclinic box is too skewed. for clarity here i am sending a part of the output file generated by the editconf God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 -0.025 0.408 -0.045 1PEGAC22 -0.015 0.326 0.084 ; 3.22000 2.60800 6.35148 0.0 0.0 0.0 0.0 -4.51376 -0.0 if i change the angles while using the editconf i observed the following changes editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 90 125.4 in this case editconf haven't given any warning and the output as follows God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 1.477 0.167 0.675 1PEGAC22 1.487 0.085 0.804 ; 3.22000 2.12585 7.79200 0.0 0.0 -1.51077 0.0 -0.0 -0.0 Can you please help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. This means equation 3.3 of the manual is not true. Maybe beta should be acute? I've no idea of necessity or convention here. Inspecting the whole output of editconf is probably instructive, but you've kept all that information to yourself instead of re-thinking how your repeat post might be constructed so as to make it easier / more likely for people help you. Likewise the final line of out_box.gro. Make sure you have read and understood what documentation is available with editconf -h and in manual section 3.2. Mark -- 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] protein folding / pbc
Correct. On Tue, Apr 10, 2012 at 1:22 PM, Shi, Huilin huil...@imail.iu.edu wrote: So if I wanna run a simulation to unfold the protein, I need make a big box that is large enough so that the unfolded protein is still smaller than the box in any dimension. Is this correct? Thanks. Huilin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Tuesday, April 10, 2012 11:54 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] protein folding / pbc On 11/04/2012 1:24 AM, Shi, Huilin wrote: Hi All, I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure. I set up pbc with the starting structure which is compact. When defining the box we use editconf and set up the -d 1.0 as the distance from the protein to the box edge. It is said that a protein should never see its periodic image. If during the simulation the protein starts unfolding, the minimum distance from the protein to the box edge will no longer be 1.0 nm. And it is possible that the length of the protein is even longer than the box dimension and the protein may see its periodic image in the neighbored box. Is this going to be a problem? Yes, if you don't allow for it from the start. Some test simulations with implicit solvent are probably priceless here. I am also confused that it is also said that (parts of) the molecule(s) diffuse out of the box is not a problem. Is this conflicted with a protein should never see its periodic image? Sometimes - can depend on orientation of molecule wrt box. Mark -- gmx-users mailing list gmx-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] martini coarse-grained
- Forwarded Message - From: dina dusti dinadu...@yahoo.com To: XAvier Periole x.peri...@rug.nl Sent: Tuesday, April 10, 2012 10:44 PM Subject: martini coarse-grained Thank you very much from your response. I found the coordinate file of tiofen from PRODRG and I wrote .itp file for that according to definition of molecules in martini_v2.1_aminoacids.itp file. What is your idea about this, Please? Best Regards Dina From: XAvier Periole x.peri...@rug.nl To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, April 10, 2012 5:16 PM Subject: Re: [gmx-users] martini coarse-grained Where did you find the topology? On Apr 10, 2012, at 10:44 AM, dina dusti wrote: Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it right? Or should I change SC5 to C-S-C for .gro file? And my definition of tiofen in .itp file it is as followed , Please say me that is it right? ;; TIOFEN [moleculetype] ; molname nrexcl TIO 1 [atoms] ; id type resnr residu atom cgnr charge 1 SC4 1 TIO SI1 1 0 2 SC5 1 TIO SI2 2 0 [constraints] ; i j funct length 1 2 1 0.27 Because I for benzene see a triangle in ngmx program, but for this see a line. Please help me to correction of mistakes. Thank you very much in advance. Best Regards Dina -- gmx-users mailing list gmx-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] Box generation for monoclinic crystal - regd
Hi Ramesh, Maybe it is easier, and less error-prone, to work in PDB format, specifying the box as a CRYST1 record. You can use the PDB format anywhere in your workflow where GRO format is used. Cheers, Tsjerk On Tue, Apr 10, 2012 at 8:13 PM, ramesh cheerla rameshgrom...@gmail.com wrote: Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 125.4 90 it gave the following warning WARNING: Triclinic box is too skewed. for clarity here i am sending a part of the output file generated by the editconf God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGA C1 1 -0.025 0.408 -0.045 1PEGA C2 2 -0.015 0.326 0.084 ; 3.22000 2.60800 6.35148 0.0 0.0 0.0 0.0 -4.51376 -0.0 if i change the angles while using the editconf i observed the following changes editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 90 125.4 in this case editconf haven't given any warning and the output as follows God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGA C1 1 1.477 0.167 0.675 1PEGA C2 2 1.487 0.085 0.804 ; 3.22000 2.12585 7.79200 0.0 0.0 -1.51077 0.0 -0.0 -0.0 Can you please help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. This means equation 3.3 of the manual is not true. Maybe beta should be acute? I've no idea of necessity or convention here. Inspecting the whole output of editconf is probably instructive, but you've kept all that information to yourself instead of re-thinking how your repeat post might be constructed so as to make it easier / more likely for people help you. Likewise the final line of out_box.gro. Make sure you have read and understood what documentation is available with editconf -h and in manual section 3.2. Mark -- gmx-users mailing list gmx-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 list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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.
Re: [gmx-users] martini coarse-grained
Hi Dina, Thiophen is a five-membered ring, like the histidine side-chain, which is modeled with three beads. And then you ought to choose the bead types such that they give good agreement with atomistic PMFs and/or partitioning of the same compound. It's very unlikely that just fiddling around a bit yields a suitable model. Cheers, Tsjerk On Tue, Apr 10, 2012 at 8:29 PM, dina dusti dinadu...@yahoo.com wrote: - Forwarded Message - From: dina dusti dinadu...@yahoo.com To: XAvier Periole x.peri...@rug.nl Sent: Tuesday, April 10, 2012 10:44 PM Subject: martini coarse-grained Thank you very much from your response. I found the coordinate file of tiofen from PRODRG and I wrote .itp file for that according to definition of molecules in martini_v2.1_aminoacids.itp file. What is your idea about this, Please? Best Regards Dina From: XAvier Periole x.peri...@rug.nl To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, April 10, 2012 5:16 PM Subject: Re: [gmx-users] martini coarse-grained Where did you find the topology? On Apr 10, 2012, at 10:44 AM, dina dusti wrote: Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it right? Or should I change SC5 to C-S-C for .gro file? And my definition of tiofen in .itp file it is as followed , Please say me that is it right? ;; TIOFEN [moleculetype] ; molname nrexcl TIO 1 [atoms] ; id type resnr residu atom cgnr charge 1 SC4 1 TIO SI1 1 0 2 SC5 1 TIO SI2 2 0 [constraints] ; i j funct length 1 2 1 0.27 Because I for benzene see a triangle in ngmx program, but for this see a line. Please help me to correction of mistakes. Thank you very much in advance. Best Regards Dina -- gmx-users mailing list gmx-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 list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Box generation for monoclinic crystal - regd
Dear Tsjerk, Thank you for your reply, I will try to work with PDB format and get back to you. On Wed, Apr 11, 2012 at 12:22 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Ramesh, Maybe it is easier, and less error-prone, to work in PDB format, specifying the box as a CRYST1 record. You can use the PDB format anywhere in your workflow where GRO format is used. Cheers, Tsjerk On Tue, Apr 10, 2012 at 8:13 PM, ramesh cheerla rameshgrom...@gmail.com wrote: Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 125.4 90 it gave the following warning WARNING: Triclinic box is too skewed. for clarity here i am sending a part of the output file generated by the editconf God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 -0.025 0.408 -0.045 1PEGAC22 -0.015 0.326 0.084 ; 3.22000 2.60800 6.35148 0.0 0.0 0.0 0.0 -4.51376 -0.0 if i change the angles while using the editconf i observed the following changes editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 90 125.4 in this case editconf haven't given any warning and the output as follows God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 1.477 0.167 0.675 1PEGAC22 1.487 0.085 0.804 ; 3.22000 2.12585 7.79200 0.0 0.0 -1.51077 0.0 -0.0 -0.0 Can you please help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. This means equation 3.3 of the manual is not true. Maybe beta should be acute? I've no idea of necessity or convention here. Inspecting the whole output of editconf is probably instructive, but you've kept all that information to yourself instead of re-thinking how your repeat post might be constructed so as to make it easier / more likely for people help you. Likewise the final line of out_box.gro. Make sure you have read and understood what documentation is available with editconf -h and in manual section 3.2. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands --
[gmx-users] Particle Insertion with Buckingham Potential
I switched the potential calculation from Lennard-Jones to Buckingham. After the switch, the simulations that I submit encounter the following error: Fatal error: Not enough memory. Failed to realloc 2812110160 byes for *bin, *bin=0x83fd1008 (called from file tpi.c, line 109). I find this puzzling since the simulations worked fine with the Lennard-Jones parameters. I see no reason why switching to Buckingham would cause a memory error. The same error occurred for three different simulation systems. Any ideas? -- 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] Box generation for monoclinic crystal - regd
On 11/04/2012 4:13 AM, ramesh cheerla wrote: Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 125.4 90 it gave the following warning WARNING: Triclinic box is too skewed. for clarity here i am sending a part of the output file generated by the editconf God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 -0.025 0.408 -0.045 1PEGAC22 -0.015 0.326 0.084 ; 3.22000 2.60800 6.35148 0.0 0.0 0.0 0.0 -4.51376 -0.0 if i change the angles while using the editconf i observed the following changes editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 90 125.4 Isn't that a totally different box? See editconf -h about -angles. Mark in this case editconf haven't given any warning and the output as follows God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 1.477 0.167 0.675 1PEGAC22 1.487 0.085 0.804 ; 3.22000 2.12585 7.79200 0.0 0.0 -1.51077 0.0 -0.0 -0.0 Can you please help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. This means equation 3.3 of the manual is not true. Maybe beta should be acute? I've no idea of necessity or convention here. Inspecting the whole output of editconf is probably instructive, but you've kept all that information to yourself instead of re-thinking how your repeat post might be constructed so as to make it easier / more likely for people help you. Likewise the final line of out_box.gro. Make sure you have read and understood what documentation is available with editconf -h and in manual section 3.2. Mark -- gmx-users mailing list gmx-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/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 mailto: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] martini coarse-grained
Hi Tsjerk, Thank you very much from your response. OK, it means that I should select SC4, SC4 and SC5 for tiophen (SC4s = C-C and SC5 = S)? On the other hand, I have 2 other structure, aniline and pyrrole. If I select three beads for both of them consist of SC4, SC4 and SP1, consequently, they become similar together!!! Please help me. Thank you very much again. Best Regards Dina From: Tsjerk Wassenaar tsje...@gmail.com To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, April 10, 2012 11:38 PM Subject: Re: [gmx-users] martini coarse-grained Hi Dina, Thiophen is a five-membered ring, like the histidine side-chain, which is modeled with three beads. And then you ought to choose the bead types such that they give good agreement with atomistic PMFs and/or partitioning of the same compound. It's very unlikely that just fiddling around a bit yields a suitable model. Cheers, Tsjerk On Tue, Apr 10, 2012 at 8:29 PM, dina dusti dinadu...@yahoo.com wrote: - Forwarded Message - From: dina dusti dinadu...@yahoo.com To: XAvier Periole x.peri...@rug.nl Sent: Tuesday, April 10, 2012 10:44 PM Subject: martini coarse-grained Thank you very much from your response. I found the coordinate file of tiofen from PRODRG and I wrote .itp file for that according to definition of molecules in martini_v2.1_aminoacids.itp file. What is your idea about this, Please? Best Regards Dina From: XAvier Periole x.peri...@rug.nl To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, April 10, 2012 5:16 PM Subject: Re: [gmx-users] martini coarse-grained Where did you find the topology? On Apr 10, 2012, at 10:44 AM, dina dusti wrote: Dear GROMACS Specialists, I have doubt about definition of tiofen ring in MARTINI CG force field. May I ask you to help me, Please? I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-C. Is it right? Or should I change SC5 to C-S-C for .gro file? And my definition of tiofen in .itp file it is as followed , Please say me that is it right? ;; TIOFEN [moleculetype] ; molname nrexcl TIO 1 [atoms] ; id type resnr residu atom cgnr charge 1 SC4 1 TIO SI1 1 0 2 SC5 1 TIO SI2 2 0 [constraints] ; i j funct length 1 2 1 0.27 Because I for benzene see a triangle in ngmx program, but for this see a line. Please help me to correction of mistakes. Thank you very much in advance. Best Regards Dina -- gmx-users mailing list gmx-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 list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands-- 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] multiple dihedral function types - regd
On 11/04/2012 3:33 AM, ramesh cheerla wrote: Dear gromacs users, For one of my residues i have two types of dihedral functions, i.e C-C dihedrals are in periodic type and C-O dihedrals are in the Ryckaert-bellemans type, now i want to generate the topology file for this residue is it possible to use the two dihedral function types for this residue. I have tried by using two different dihedraltypes directives one is for the periodic type and another one is for Ryckaert-Bellemans function, but how can i incorporate the two functional types in the dihedrals section of the bondedtypes directive in aminoacids.rtp. You can't. That is a limitation of pdb2gmx. or is there any methods in gromacs to convert one dihedral functional form to the other. Basic trig will let you express a periodic dihedral of sufficiently small periodicity in R-B form. However that's only a reasonable solution with pdb2gmx if the force field uses only R-B dihedrals. It may be more effective to use pdb2gmx and to replace the inappropriate dihedral form in the .top file by hand afterwards. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Can gromacs handle reflective boundary condition ?
On 10/04/2012 11:50 PM, stjohn55 wrote: Dear, Can gromacs handle reflective boundary condition, in order to remove the periodicity of Z-axis ? No. Mark Do I need to take advantage of walls and Ewald ? Thanks so much! Yours, John Yu 2012.04.10 -- 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] multiple dihedral function types - regd
Thank you mark. On Wed, Apr 11, 2012 at 8:09 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/04/2012 3:33 AM, ramesh cheerla wrote: Dear gromacs users, For one of my residues i have two types of dihedral functions, i.e C-C dihedrals are in periodic type and C-O dihedrals are in the Ryckaert-bellemans type, now i want to generate the topology file for this residue is it possible to use the two dihedral function types for this residue. I have tried by using two different dihedraltypes directives one is for the periodic type and another one is for Ryckaert-Bellemans function, but how can i incorporate the two functional types in the dihedrals section of the bondedtypes directive in aminoacids.rtp. You can't. That is a limitation of pdb2gmx. or is there any methods in gromacs to convert one dihedral functional form to the other. Basic trig will let you express a periodic dihedral of sufficiently small periodicity in R-B form. However that's only a reasonable solution with pdb2gmx if the force field uses only R-B dihedrals. It may be more effective to use pdb2gmx and to replace the inappropriate dihedral form in the .top file by hand afterwards. Mark -- 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] Box generation for monoclinic crystal - regd
Thank you mark. On Wed, Apr 11, 2012 at 6:15 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/04/2012 4:13 AM, ramesh cheerla wrote: Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 125.4 90 it gave the following warning WARNING: Triclinic box is too skewed. for clarity here i am sending a part of the output file generated by the editconf God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 -0.025 0.408 -0.045 1PEGAC22 -0.015 0.326 0.084 ; 3.22000 2.60800 6.35148 0.0 0.0 0.0 0.0 -4.51376 -0.0 if i change the angles while using the editconf i observed the following changes editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 90 125.4 Isn't that a totally different box? See editconf -h about -angles. Mark in this case editconf haven't given any warning and the output as follows God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 1.477 0.167 0.675 1PEGAC22 1.487 0.085 0.804 ; 3.22000 2.12585 7.79200 0.0 0.0 -1.51077 0.0 -0.0 -0.0 Can you please help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. This means equation 3.3 of the manual is not true. Maybe beta should be acute? I've no idea of necessity or convention here. Inspecting the whole output of editconf is probably instructive, but you've kept all that information to yourself instead of re-thinking how your repeat post might be constructed so as to make it easier / more likely for people help you. Likewise the final line of out_box.gro. Make sure you have read and understood what documentation is available with editconf -h and in manual section 3.2. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] regarding micelle and its analysis
hello sir, i am studying about micelle formation of surfactants. i performed my run for 10ns.. when i visualize my final md pdb file i got around 2 to 3 micelles. my doubt is while performing analysis , g_gyrate giving a value of around 3nm.. this value corresponds to which micelle.. how its calculating this value.. please help me with your answer.. i am so confused with my analysis.. thanking you, -- 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
