<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi Justin<br><br>Thanks a lot for your prompt reply.<br>The end of the em log file says:<br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 10<br><br>Double precision normally gives you higher accuracy.<br><br>Steepest Descents converged to machine precision in 206 steps,<br>but did not reach the requested Fmax < 10.<br>Potential Energy = -1.8784400e+05<br>Maximum force = 7.9173694e+02 on atom 159<br>Norm of force = 6.5868745e+03<br><br>And after em, I ran pr for 2ns and it went all good and you're correct it was for all bonds. <br>After I read the manual and a couple of tutorial I understood that the PME is better for electrostatics but I am reproducing a reported work that used twin range cutoff of 1 for both vdw
and electrostatics using 2fs time step and I want to see if I will get similar results. The authors stated that the simulations went well till the end of the 25 ns run! But seems that mine is crashing. Any suggestions?<br><br>Thanks<br><br><span style="color: rgb(0, 0, 191); font-family: tahoma,new york,times,serif;">Rabab Toubar</span><br style="color: rgb(0, 0, 191); font-family: tahoma,new york,times,serif;"><br><br>--- On <b>Fri, 6/4/10, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] 1-4 interaction not within cut-off<br>To: "Gromacs Users' List" <gmx-users@gromacs.org><br>Date: Friday, June 4, 2010, 3:25 PM<br><br><div class="plainMail"><br><br>Rabab Toubar wrote:<br>> Hi Justin,<br>> <br>> Thanks for the reply. When I tried to gmxcheck the
minimization process I got an error:<br>> <br>> Timesteps at t=810 don't match (2, 1)<br>> <br>> Timesteps at t=814 don't match (1, 2)<br>> <br>> Timesteps at t=816 don't match (2, 1)<br>> <br>> Timesteps at t=818 don't match (1, 2)<br>> <br>> till the end of the run, that is why I thought the system is not properly minimized. I will look into how to check the Potential Energy.<br>> <br><br>When running EM, mdrun prints the important information out at the very end, both to the screen and to the end of the .log file.<br><br><br>> the em.mdp file is as follows:<br>> cpp = /usr/bin/cpp ; the c preprocessor<br>> define = -DFLEXIBLE<br>> constraints = none<br>> integrator = steep<br>> dt = 0.002 ;ps ie 2 fs!<br>> nsteps = 1000<br>>
nstlist = 10 ns_type = grid<br>> rlist = 1.0 ;short range<br>> coulombtype = cut-off<br>> rcoulomb = 1.0 rvdw = 1.0<br>> vdwtype = cut-off fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> pme_order = 4<br>> ewald_rtol = 1e-5<br>> optimize_fft = yes emtol = 10 emstep = 0.01<br>> <br>> the md.mdp file is:<br>> cpp = /usr/bin/cpp<br>> constraints = none
;*<br>> integrator = md<br>> dt = 0.002 ; ps !<br><br>Using a 2-fs timestep without constraints may not be stable. Your original message said you ran 2 ns of position restrained MD with LINCS, which I assumed meant that you were constraining the bond lengths. If you actually did this, what reason do you have for turning off the restraints after equilibrating?<br><br>> nsteps = 12500000 ; total 25 ns;*<br>> nstcomm = 1<br>> nstxout = 500 ; collect data every 1 ps<br>> nstvout = 0<br>> nstfout
= 0<br>> nstlist = 10<br>> ns_type = grid<br>> rlist = 1.0<br>> coulombtype = cut-off<br><br>Using a plain cutoff for electrostatics can lead to a number of artefacts. I see no reason to use this method in favor of other, more advanced and accurate methods.<br><br>-Justin<br><br>> rcoulomb = 1.0<br>> vdwtype = cut-off<br>> rvdw = 1.0 ;*<br>> fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny
= 0<br>> fourier_nz = 0<br>> pme_order = 4<br>> ewald_rtol = 1e-5<br>> optimize_fft = yes <br>> ; Berendsen temperature coupling is on<br>> Tcoupl = berendsen<br>> tau_t = 0.1 0.1<br>> tc-grps = protein non-protein ref_t = 300 300<br>> <br>> ; Pressure coupling is on<br>> Pcoupl = berendsen<br>> pcoupltype =
isotropic<br>> tau_p = 0.5 ; ps<br>> compressibility = 4.5e-5 ; bar-1<br>> ref_p = 1.0<br>> <br>> ; Generate velocites is on at 300 K.<br>> gen_vel = yes<br>> gen_temp = 300.0<br>> gen_seed = 621432<br>> <br>> Any suggestions are appreciated<br>> <br>> Thanks<br>> Rabab Toubar<br>> <br>> <br>> --- On *Thu, 6/3/10, Justin A. Lemkul /<<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>>/* wrote:<br>> <br>> <br>> From: Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu"
href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> Subject: Re: [gmx-users] 1-4 interaction not within cut-off<br>> To: "Discussion list for GROMACS users" <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Date: Thursday, June 3, 2010, 4:37 PM<br>> <br>> <br>> <br>> Rabab Toubar wrote:<br>> > Hi,<br>> ><br>> > I set my .mdp file to minimize the system for 1000 steps, but it<br>> stopped at ~200 saying: "Stepsize too small, or no change in energy.<br>> > Converged to machine precision, but not to the requested<br>> precision Fmax < 10" but the molecule is now outside the box<br>>
><br>> <br>> This is not really a problem, provided that both the potential<br>> energy and Fmax that resulted are<br>> reasonable.<a href="http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision" target="_blank">http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision</a><br>> <br>> > I did position restraint for 2ns using LINCS, and things went well<br>> ><br>> > running md, it ran for only 0.3 ns out of 30, and I got an error<br>> message that 1-4 interaction between 2 atoms are at a distance ><br>> table-size
(1nm) with a suggestion to increase the table-extension<br>> in mdp file.<br>> > I checked <a href="http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off" target="_blank">http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off</a><br>> suggesting reminimizing.<br>> ><br>> <br>> The other possibility is that your .mdp settings are inappropriate,<br>> but you haven't provided that information.<br>> <br>> > My question is: is it OK that the system doesn't minimize till<br>> the end of the specified number of steps? is it OK to be outside the<br>> box as long as you assign boundary conditions as in case of NAMD?<br>>
and what is the best option - you think - I have to solve the md problem<br>> ><br>> <br>> Whether or not you need to revisit the EM procedure depends on how<br>> well it actually did (see comment above). The periodicity effect is<br>> a non-issue, since there is no "outside" of a periodic box.<br>> <br>> <a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>> <br>> -Justin<br>> <br>> > Any suggestions are highly apprecitaed<br>> > Rabab<br>> ><br>> ><br>> <br>> --
========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a
href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>> posting!<br>> Please don't post (un)subscribe requests to the list. Use the www<br>> interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT
Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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