[gmx-users] Re: gmx-users Digest, Vol 86, Issue 143
marco miele
marco.miele75 at gmail.com
Thu Jun 23 07:09:21 CEST 2011
2011/6/23 <gmx-users-request at gromacs.org>
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> Today's Topics:
>
> 1. Re: DPPC temperatur setting (Justin A. Lemkul)
> 2. Timing variability (chris.neale at 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] DPPC temperatur setting
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E0217E2.2000209 at 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.neale at utoronto.ca
> Subject: [gmx-users] Timing variability
> To: gmx-users at gromacs.org
> Message-ID: <20110622123216.49pl7396u8k880oo at 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.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Timing variability
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E021C06.3050807 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 23/06/2011 2:32 AM, chris.neale at 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 <hmkvsri at gmail.com>
> Subject: [gmx-users] Trajectory and ED - (not old question again)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTimMmZQcuAexfGbs_veFtg5s61qc0w at 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
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> ------------------------------
>
> Message: 5
> Date: Wed, 22 Jun 2011 17:48:28 -0400
> From: Ye Yang <knightyangpku at gmail.com>
> Subject: [gmx-users]Question about reduced unit for coarse grain
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTimxfqVMT9ha9sHE=+ANKEfwAQSrPQ at 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
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> ------------------------------
>
> Message: 6
> Date: Wed, 22 Jun 2011 18:15:51 -0400
> From: Zack Scholl <zns at duke.edu>
> Subject: [gmx-users] Relaxed frozen groups
> To: gmx-users at gromacs.org
> Message-ID: <BANLkTimrMdP_hxJLMetFhQscgi4fJqsX0w at 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
>
>
> ------------------------------
>
> --
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> Please search the archive at
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>
> End of gmx-users Digest, Vol 86, Issue 143
> ******************************************
>
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