2011/6/23 <gmx-users-requ...@gromacs.org> > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: DPPC temperatur setting (Justin A. Lemkul) > 2. Timing variability (chris.ne...@utoronto.ca) > 3. Re: Timing variability (Mark Abraham) > 4. Trajectory and ED - (not old question again) (Kavyashree M) > 5. [gmx-users]Question about reduced unit for coarse grain (Ye Yang) > 6. Relaxed frozen groups (Zack Scholl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Jun 2011 12:27:14 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] DPPC temperatur setting > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e0217e2.2000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > marco miele wrote: > > Please heed this: > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of gmx-users digest..." > > > > ...and don't reply to the entire digest. I just stated the reasons a few > minutes ago and won't bother to repeat myself again here. > > <snip> > > > marco miele wrote: > > > Hi everybody > > > I am starting to analyze the membrane system composed with DPPC > > lipids, > > > I saw both MD membrane paper and KALP-15 tutorial to setting a > 323K. > > > My question is That > > > in this way we working around 50 C, which is not body temperature > > 37 C, > > > this is not realistic approach, > > > If my interest is to obtain data that respects the human body > > condition > > > can I to setting the temperature at 310 = 37 C or a make mistake > and > > > obtain artefacts data. > > > > > > > The reason for using 323 K in the case of DPPC is that (1) it is a > > common > > experimental temperature and (2) it is above the phase-transition > > temperature > > for this lipid. Anywhere below 315 K or so and your membrane will > > enter a gel > > phase, which is not representative of the membrane properties in > > vivo. Working > > with DPPC thus involves a tradeoff - you can either produce a liquid > > phase (like > > in vivo) or physiological temperature (while losing the physical > > properties > > associated with cellular membranes). The latter is often > > disfavored, but the > > end result is that DPPC is simply a poor choice to represent cell > > membranes, but > > is often a useful in vitro model, depending on your aims and > > available data. > > > > -Justin > > > > > > > > My aim is to obtain a good model for analyzing a receptor protein (not > > channel). > > I prepared a system with DPPC CHOL and Protein, but I am not sure fore > > only temperature. > > > > "The latter is often disfavored, but the end result is that DPPC is > > simply a poor choice to represent cell membranes, > > but is often a useful in vitro model, depending on your aims and > > available data." > > > > What kind of lipid you suggest me, in vision of system indicated before > > DPPC CHOL PROTEIN. > > I am interesting to understand if the conformation of protein is > > mantained in diff % of CHOL. > > > > Well, if you're convinced you want to model DPPC/cholesterol membranes, > then I'm > not going to try to suggest you do anything else. Only you know what your > goals > are and what experimental observables you're trying to reproduce or expand > upon. > A DPPC/cholesterol mixture does not represent human cell membranes very > well, > but this information is specific to different cell types. > > If you just want to measure the effects of cholesterol on some arbitrary > lipid > model, then it doesn't much matter what you use, but you'll have to deal > with > the assumption that pure DPPC would inherently be in the gel phase in vivo. > Cholesterol will augment this effect, so it is hard to say what temperature > you > should use. If you state the assumption that pure DPPC should be simulated > at > roughly 323 K and everything is relative to that, it's part of the > interpretation of your results. > > -Justin > > I'm interested to analyze conformational change of receptor protein embedded in membrane. I already performed a dynamic whit only DPPC I utilized this lipid to see as it influence the conformation of protein, but I want to realyze a experiment that simulate the membrane as realistic as possible. In my first MD with DPPC/protein I found that my protein receptor tends to increase the helices sizte, someone of the 7 helix tend pass from alfa helix in p-helix and so on. I performed MD at 323 K 1 amt, my protocoll is like your tutorial on KALP-15.
"A DPPC/cholesterol mixture does not represent human cell membranes very well, but this information is specific to different cell types. But now I have some doubts on the use of lipid DPPC is not suitable to build my realistic model, what you tink if I substitute it with DOPC. Cholesterol will augment this effect, so it is hard to say what temperature you should use. I work on 323K in this way I obtain the transition face for DPPC. I want just to see as the cholesterol influece the the "solvent" DPPC for my proteins ( sorry for my english. I hope that you understand wath I mean) If you state the assumption that pure DPPC should be simulated at roughly 323 K and everything is relative to that, it's part of the interpretation of your results. I want to know if I add cholesterol in DPPC membrane wath happen at protein receptor and if the chol tend to clustering with the protein receptor, I want to performing different MD with different % of CHOL. thank you your adivice open my mind. -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > Message: 2 > Date: Wed, 22 Jun 2011 12:32:16 -0400 > From: chris.ne...@utoronto.ca > Subject: [gmx-users] Timing variability > To: gmx-users@gromacs.org > Message-ID: <20110622123216.49pl7396u8k88...@webmail.utoronto.ca> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear Users: > > Has anybody else looked at simulation speed (ns/day) over the segments > of long runs? I always benchmark and optimize my systems carefully, > but it was only recently that I realized how much variability I am > obtaining over long runs. Perhaps this is specific to my cluster, > which is one reason for my post. > > Here is the performance (in ns/day) that I obtain with a single run. > This is representative of what I see with 30 other runs (see list > below). First, the distribution is bimodal, with peaks at around 80 > and 90 ns/day. Second, the values go as low as 70 ns/day (and I have > seen as low as 50 ns/day when I look through all 30 run directories > that differ only by the position of the umbrella restraint). > > I am using gromacs 4.5.3 and I run it like this: > mpirun mdrun_mpi -deffnm md1 -dlb yes -npme 16 -cpt 30 -maxh 47 -cpi > md1.cpt -cpo md1.cpt -px coord.xvg -pf force.xvg -noappend > > I have obtained similar behaviour also with another system. > > I have attempted to correlate timing with the node on which the job > runs, the output of the "^Grid:" in the .log file, the DD division of > PME and real-space and the value of pme mesh/force, all to no avail. I > have found one correlation whereby the very slow runs also indicate a > high relative load for PME. > > I suspect that it is some value that is being determined at run start > time that is affecting my performance, but I am not sure what this > could be. Perhaps the fourier-spacing is leading to different initial > grids? > > Thank you (timing information and my .mdp file follows), > Chris > > ########### Output the ns/day obtained by the run segments > $ grep Perf *log|awk '{print $4}' > > 78.286 > 82.345 > 81.573 > 83.418 > 92.423 > 90.863 > 85.833 > 91.131 > 91.820 > 71.246 > 76.844 > 91.805 > 92.037 > 85.702 > 92.251 > 89.706 > 88.590 > 89.381 > 90.446 > 81.142 > 76.365 > 76.968 > 76.037 > 79.286 > 79.895 > 79.047 > 78.273 > 79.406 > 78.018 > 78.645 > 78.172 > 80.255 > 81.032 > 81.047 > 77.414 > 78.414 > 80.167 > 79.278 > 80.892 > 82.796 > 81.300 > 77.392 > 71.350 > 73.134 > 76.519 > 75.879 > 80.684 > 81.076 > 87.821 > 90.064 > 88.409 > 80.803 > 88.435 > > ########### My .mdp file > > constraints = all-bonds > lincs-iter = 1 > lincs-order = 6 > constraint_algorithm = lincs > integrator = sd > dt = 0.004 > tinit = 1000000 > init_step = 0 > nsteps = 1000000000 > nstcomm = 1 > nstxout = 1000000000 > nstvout = 1000000000 > nstfout = 1000000000 > nstxtcout = 25000 > nstenergy = 25000 > nstlist = 5 > nstlog=0 ; reduce log file size > ns_type = grid > rlist = 1 > rcoulomb = 1 > rvdw = 1 > coulombtype = PME > ewald-rtol = 1e-5 > optimize_fft = yes > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > tc_grps = System > tau_t = 1.0 > ld_seed = -1 > ref_t = 300 > gen_temp = 300 > gen_vel = yes > unconstrained_start = no > gen_seed = -1 > Pcoupl = berendsen > pcoupltype = semiisotropic > tau_p = 4 4 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > > ; COM PULLING > pull = umbrella > pull_geometry = position > pull_dim = N N Y > pull_start = no > pull_nstxout = 250 > pull_nstfout = 250 > pull_ngroups = 1 > pull_group0 = POPC > pull_pbcatom0 = 338 > pull_group1 = KSC > pull_pbcatom1 = 0 > pull_init1 = 0 0 0.0 > pull_rate1 = 0 > pull_k1 = 3000.0 > pull_vec1 = 0 0 0 > ;;;EOF > > > > > ------------------------------ > > Message: 3 > Date: Thu, 23 Jun 2011 02:44:54 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] Timing variability > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4e021c06.3050...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 23/06/2011 2:32 AM, chris.ne...@utoronto.ca wrote: > > Dear Users: > > > > Has anybody else looked at simulation speed (ns/day) over the segments > > of long runs? I always benchmark and optimize my systems carefully, > > but it was only recently that I realized how much variability I am > > obtaining over long runs. Perhaps this is specific to my cluster, > > which is one reason for my post. > > You can get random and large hits if someone else is sharing your > network (yes, even Infiniband) and hitting it hard enough. You can > sort-of diagnose this after the fact by looking at the breakdown of > GROMACS timings and seeing where runs spend their time. diff -y -W 160 > can be useful here. Look at the MPMD flowchart in the manual (Figure > 3.15) to get an idea which parts match up with what lines. > > Speak with your admins and learn what you can. You might be able to > mitigate the effects by using fewer processors, so that your > computation/communication ratio goes up. Your throughput is lower, but > your efficiency is higher. Or beg for dedicated network space to see > what quiet-conditions performance looks like. > > > Here is the performance (in ns/day) that I obtain with a single run. > > This is representative of what I see with 30 other runs (see list > > below). First, the distribution is bimodal, with peaks at around 80 > > and 90 ns/day. Second, the values go as low as 70 ns/day (and I have > > seen as low as 50 ns/day when I look through all 30 run directories > > that differ only by the position of the umbrella restraint). > > > > I am using gromacs 4.5.3 and I run it like this: > > mpirun mdrun_mpi -deffnm md1 -dlb yes -npme 16 -cpt 30 -maxh 47 -cpi > > md1.cpt -cpo md1.cpt -px coord.xvg -pf force.xvg -noappend > > > > I have obtained similar behaviour also with another system. > > > > I have attempted to correlate timing with the node on which the job > > runs, the output of the "^Grid:" in the .log file, the DD division of > > PME and real-space and the value of pme mesh/force, all to no avail. I > > have found one correlation whereby the very slow runs also indicate a > > high relative load for PME. > > That is suggestive of network noise - PME requires global > intra-simulation communication. > > > I suspect that it is some value that is being determined at run start > > time that is affecting my performance, but I am not sure what this > > could be. Perhaps the fourier-spacing is leading to different initial > > grids? > > I don't think "optimize_fft = yes" does much any more - but you can > verify that by inspection of the start of the log file. > > Mark > > > Thank you (timing information and my .mdp file follows), > > Chris > > > > ########### Output the ns/day obtained by the run segments > > $ grep Perf *log|awk '{print $4}' > > > > 78.286 > > 82.345 > > 81.573 > > 83.418 > > 92.423 > > 90.863 > > 85.833 > > 91.131 > > 91.820 > > 71.246 > > 76.844 > > 91.805 > > 92.037 > > 85.702 > > 92.251 > > 89.706 > > 88.590 > > 89.381 > > 90.446 > > 81.142 > > 76.365 > > 76.968 > > 76.037 > > 79.286 > > 79.895 > > 79.047 > > 78.273 > > 79.406 > > 78.018 > > 78.645 > > 78.172 > > 80.255 > > 81.032 > > 81.047 > > 77.414 > > 78.414 > > 80.167 > > 79.278 > > 80.892 > > 82.796 > > 81.300 > > 77.392 > > 71.350 > > 73.134 > > 76.519 > > 75.879 > > 80.684 > > 81.076 > > 87.821 > > 90.064 > > 88.409 > > 80.803 > > 88.435 > > > > ########### My .mdp file > > > > constraints = all-bonds > > lincs-iter = 1 > > lincs-order = 6 > > constraint_algorithm = lincs > > integrator = sd > > dt = 0.004 > > tinit = 1000000 > > init_step = 0 > > nsteps = 1000000000 > > nstcomm = 1 > > nstxout = 1000000000 > > nstvout = 1000000000 > > nstfout = 1000000000 > > nstxtcout = 25000 > > nstenergy = 25000 > > nstlist = 5 > > nstlog=0 ; reduce log file size > > ns_type = grid > > rlist = 1 > > rcoulomb = 1 > > rvdw = 1 > > coulombtype = PME > > ewald-rtol = 1e-5 > > optimize_fft = yes > > fourierspacing = 0.12 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > pme_order = 4 > > tc_grps = System > > tau_t = 1.0 > > ld_seed = -1 > > ref_t = 300 > > gen_temp = 300 > > gen_vel = yes > > unconstrained_start = no > > gen_seed = -1 > > Pcoupl = berendsen > > pcoupltype = semiisotropic > > tau_p = 4 4 > > compressibility = 4.5e-5 4.5e-5 > > ref_p = 1.0 1.0 > > > > ; COM PULLING > > pull = umbrella > > pull_geometry = position > > pull_dim = N N Y > > pull_start = no > > pull_nstxout = 250 > > pull_nstfout = 250 > > pull_ngroups = 1 > > pull_group0 = POPC > > pull_pbcatom0 = 338 > > pull_group1 = KSC > > pull_pbcatom1 = 0 > > pull_init1 = 0 0 0.0 > > pull_rate1 = 0 > > pull_k1 = 3000.0 > > pull_vec1 = 0 0 0 > > ;;;EOF > > > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 22 Jun 2011 22:52:45 +0530 > From: Kavyashree M <hmkv...@gmail.com> > Subject: [gmx-users] Trajectory and ED - (not old question again) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <banlktimmmzqcuaexfgbs_veftg5s61q...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear users, > > I did ED analysis for one of the trajectories, > when I visualised the trajectory along the first > five eigen vectors using g_nmtraj it does not > show much movements. It was a simulation of > 100 ns. > My doubt is when I visualise the trajectory in > pymol calculated just after simulation I could > observe large movements in certain regions. > same regions do have movements in ED > trajectory also but not as large as this. > Why is this? > > Thank you > With Regards > M. Kavyashree > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110622/25496797/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 22 Jun 2011 17:48:28 -0400 > From: Ye Yang <knightyang...@gmail.com> > Subject: [gmx-users]Question about reduced unit for coarse grain > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <BANLkTimxfqVMT9ha9sHE=+ankefwaqs...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all: > I see from the user's manual that if our input is in reduced unit, > the output will also be in reduced unit(, > ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf), P25. On the > contrary, if we use standard unit, the out put will be in standard unit. > This brings the question up when we use coarse grain Clementi's > model webtool (http://smog.ucsd.edu/sbm_faq.html), according to the > author, > it seems that everything is in reduced unit, so the output file should also > be in reduced unit, yet I found the topology file that the energy unit is > KJ/mol. What exactly is the unit of the input and out put file? When I pull > the molecules, do I get the reduced unit result or the physical unit > result? > Since I am an experimentalist, getting the physical units is more > important to me, so as to compare with the experimental results, albeit the > intrinsic difference. If I get something in reduced unit, there is > necessity > for me to change it into physical unit, or at least clarify it in > comparison. > Thank you very much. > > Ye > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110622/b40c7891/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Wed, 22 Jun 2011 18:15:51 -0400 > From: Zack Scholl <z...@duke.edu> > Subject: [gmx-users] Relaxed frozen groups > To: gmx-users@gromacs.org > Message-ID: <banlktimrmdp_hxjlmetfhqscgi4fjqs...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all- > > Is it possible to freeze a group of atoms only partially in a > direction? For instance, could I freeze a group inside a box of a > definite size? > > > Sincere thanks, > > Zack > > > ------------------------------ > > -- > 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! > > End of gmx-users Digest, Vol 86, Issue 143 > ****************************************** >
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