<br><br><div class="gmail_quote">2011/6/23 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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Today's Topics:<br>
<br>
1. Re: DPPC temperatur setting (Justin A. Lemkul)<br>
2. Timing variability (<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>)<br>
3. Re: Timing variability (Mark Abraham)<br>
4. Trajectory and ED - (not old question again) (Kavyashree M)<br>
5. [gmx-users]Question about reduced unit for coarse grain (Ye Yang)<br>
6. Relaxed frozen groups (Zack Scholl)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 22 Jun 2011 12:27:14 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] DPPC temperatur setting<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E0217E2.2000209@vt.edu">4E0217E2.2000209@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
marco miele wrote:<br>
<br>
Please heed this:<br>
<br>
> When replying, please edit your Subject line so it is more specific<br>
> than "Re: Contents of gmx-users digest..."<br>
><br>
<br>
...and don't reply to the entire digest. I just stated the reasons a few<br>
minutes ago and won't bother to repeat myself again here.<br>
<br>
<snip><br>
<br>
> marco miele wrote:<br>
> > Hi everybody<br>
> > I am starting to analyze the membrane system composed with DPPC<br>
> lipids,<br>
> > I saw both MD membrane paper and KALP-15 tutorial to setting a 323K.<br>
> > My question is That<br>
> > in this way we working around 50 C, which is not body temperature<br>
> 37 C,<br>
> > this is not realistic approach,<br>
> > If my interest is to obtain data that respects the human body<br>
> condition<br>
> > can I to setting the temperature at 310 = 37 C or a make mistake and<br>
> > obtain artefacts data.<br>
> ><br>
><br>
> The reason for using 323 K in the case of DPPC is that (1) it is a<br>
> common<br>
> experimental temperature and (2) it is above the phase-transition<br>
> temperature<br>
> for this lipid. Anywhere below 315 K or so and your membrane will<br>
> enter a gel<br>
> phase, which is not representative of the membrane properties in<br>
> vivo. Working<br>
> with DPPC thus involves a tradeoff - you can either produce a liquid<br>
> phase (like<br>
> in vivo) or physiological temperature (while losing the physical<br>
> properties<br>
> associated with cellular membranes). The latter is often<br>
> disfavored, but the<br>
> end result is that DPPC is simply a poor choice to represent cell<br>
> membranes, but<br>
> is often a useful in vitro model, depending on your aims and<br>
> available data.<br>
><br>
> -Justin<br>
><br>
><br>
><br>
> My aim is to obtain a good model for analyzing a receptor protein (not<br>
> channel).<br>
> I prepared a system with DPPC CHOL and Protein, but I am not sure fore<br>
> only temperature.<br>
><br>
> "The latter is often disfavored, but the end result is that DPPC is<br>
> simply a poor choice to represent cell membranes,<br>
> but is often a useful in vitro model, depending on your aims and<br>
> available data."<br>
><br>
> What kind of lipid you suggest me, in vision of system indicated before<br>
> DPPC CHOL PROTEIN.<br>
> I am interesting to understand if the conformation of protein is<br>
> mantained in diff % of CHOL.<br>
><br>
<br>
Well, if you're convinced you want to model DPPC/cholesterol membranes, then I'm<br>
not going to try to suggest you do anything else. Only you know what your goals<br>
are and what experimental observables you're trying to reproduce or expand upon.<br>
A DPPC/cholesterol mixture does not represent human cell membranes very well,<br>
but this information is specific to different cell types.<br>
<br>
If you just want to measure the effects of cholesterol on some arbitrary lipid<br>
model, then it doesn't much matter what you use, but you'll have to deal with<br>
the assumption that pure DPPC would inherently be in the gel phase in vivo.<br>
Cholesterol will augment this effect, so it is hard to say what temperature you<br>
should use. If you state the assumption that pure DPPC should be simulated at<br>
roughly 323 K and everything is relative to that, it's part of the<br>
interpretation of your results.<br>
<br>
-Justin<br>
<br></blockquote><div> </div><div>I'm interested to analyze conformational change of receptor protein<br>embedded in membrane. I already performed a dynamic whit only DPPC<br>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.<br>
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.<br>
<br><span style="color: rgb(204, 51, 204);">"A DPPC/cholesterol mixture does not represent human cell membranes very well, </span><span style="color: rgb(204, 51, 204);">but this information is specific to different cell types.</span><br>
<br>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.<br><br style="color: rgb(153, 51, 153);"><span style="color: rgb(153, 51, 153);">Cholesterol will augment this effect, so it is hard to say what temperature you </span><span style="color: rgb(153, 51, 153);">should use. <br>
<br><font color="#000000">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)</font><br>
<br>If you state the assumption that pure DPPC should be simulated at </span><span style="color: rgb(153, 51, 153);">roughly 323 K and everything is relative to that, it's part of the</span><br style="color: rgb(153, 51, 153);">
<span style="color: rgb(153, 51, 153);">
interpretation of your results.</span><br>
<br>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. <br><br>thank you your adivice open my mind.<br><br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
--<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]<a href="http://vt.edu" target="_blank">vt.edu</a> | (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>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 22 Jun 2011 12:32:16 -0400<br>
From: <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a><br>
Subject: [gmx-users] Timing variability<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:20110622123216.49pl7396u8k880oo@webmail.utoronto.ca">20110622123216.49pl7396u8k880oo@webmail.utoronto.ca</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";<br>
format="flowed"<br>
<br>
Dear Users:<br>
<br>
Has anybody else looked at simulation speed (ns/day) over the segments<br>
of long runs? I always benchmark and optimize my systems carefully,<br>
but it was only recently that I realized how much variability I am<br>
obtaining over long runs. Perhaps this is specific to my cluster,<br>
which is one reason for my post.<br>
<br>
Here is the performance (in ns/day) that I obtain with a single run.<br>
This is representative of what I see with 30 other runs (see list<br>
below). First, the distribution is bimodal, with peaks at around 80<br>
and 90 ns/day. Second, the values go as low as 70 ns/day (and I have<br>
seen as low as 50 ns/day when I look through all 30 run directories<br>
that differ only by the position of the umbrella restraint).<br>
<br>
I am using gromacs 4.5.3 and I run it like this:<br>
mpirun mdrun_mpi -deffnm md1 -dlb yes -npme 16 -cpt 30 -maxh 47 -cpi<br>
md1.cpt -cpo md1.cpt -px coord.xvg -pf force.xvg -noappend<br>
<br>
I have obtained similar behaviour also with another system.<br>
<br>
I have attempted to correlate timing with the node on which the job<br>
runs, the output of the "^Grid:" in the .log file, the DD division of<br>
PME and real-space and the value of pme mesh/force, all to no avail. I<br>
have found one correlation whereby the very slow runs also indicate a<br>
high relative load for PME.<br>
<br>
I suspect that it is some value that is being determined at run start<br>
time that is affecting my performance, but I am not sure what this<br>
could be. Perhaps the fourier-spacing is leading to different initial<br>
grids?<br>
<br>
Thank you (timing information and my .mdp file follows),<br>
Chris<br>
<br>
########### Output the ns/day obtained by the run segments<br>
$ grep Perf *log|awk '{print $4}'<br>
<br>
78.286<br>
82.345<br>
81.573<br>
83.418<br>
92.423<br>
90.863<br>
85.833<br>
91.131<br>
91.820<br>
71.246<br>
76.844<br>
91.805<br>
92.037<br>
85.702<br>
92.251<br>
89.706<br>
88.590<br>
89.381<br>
90.446<br>
81.142<br>
76.365<br>
76.968<br>
76.037<br>
79.286<br>
79.895<br>
79.047<br>
78.273<br>
79.406<br>
78.018<br>
78.645<br>
78.172<br>
80.255<br>
81.032<br>
81.047<br>
77.414<br>
78.414<br>
80.167<br>
79.278<br>
80.892<br>
82.796<br>
81.300<br>
77.392<br>
71.350<br>
73.134<br>
76.519<br>
75.879<br>
80.684<br>
81.076<br>
87.821<br>
90.064<br>
88.409<br>
80.803<br>
88.435<br>
<br>
########### My .mdp file<br>
<br>
constraints = all-bonds<br>
lincs-iter = 1<br>
lincs-order = 6<br>
constraint_algorithm = lincs<br>
integrator = sd<br>
dt = 0.004<br>
tinit = 1000000<br>
init_step = 0<br>
nsteps = 1000000000<br>
nstcomm = 1<br>
nstxout = 1000000000<br>
nstvout = 1000000000<br>
nstfout = 1000000000<br>
nstxtcout = 25000<br>
nstenergy = 25000<br>
nstlist = 5<br>
nstlog=0 ; reduce log file size<br>
ns_type = grid<br>
rlist = 1<br>
rcoulomb = 1<br>
rvdw = 1<br>
coulombtype = PME<br>
ewald-rtol = 1e-5<br>
optimize_fft = yes<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
tc_grps = System<br>
tau_t = 1.0<br>
ld_seed = -1<br>
ref_t = 300<br>
gen_temp = 300<br>
gen_vel = yes<br>
unconstrained_start = no<br>
gen_seed = -1<br>
Pcoupl = berendsen<br>
pcoupltype = semiisotropic<br>
tau_p = 4 4<br>
compressibility = 4.5e-5 4.5e-5<br>
ref_p = 1.0 1.0<br>
<br>
; COM PULLING<br>
pull = umbrella<br>
pull_geometry = position<br>
pull_dim = N N Y<br>
pull_start = no<br>
pull_nstxout = 250<br>
pull_nstfout = 250<br>
pull_ngroups = 1<br>
pull_group0 = POPC<br>
pull_pbcatom0 = 338<br>
pull_group1 = KSC<br>
pull_pbcatom1 = 0<br>
pull_init1 = 0 0 0.0<br>
pull_rate1 = 0<br>
pull_k1 = 3000.0<br>
pull_vec1 = 0 0 0<br>
;;;EOF<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 23 Jun 2011 02:44:54 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Timing variability<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E021C06.3050807@anu.edu.au">4E021C06.3050807@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 23/06/2011 2:32 AM, <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a> wrote:<br>
> Dear Users:<br>
><br>
> Has anybody else looked at simulation speed (ns/day) over the segments<br>
> of long runs? I always benchmark and optimize my systems carefully,<br>
> but it was only recently that I realized how much variability I am<br>
> obtaining over long runs. Perhaps this is specific to my cluster,<br>
> which is one reason for my post.<br>
<br>
You can get random and large hits if someone else is sharing your<br>
network (yes, even Infiniband) and hitting it hard enough. You can<br>
sort-of diagnose this after the fact by looking at the breakdown of<br>
GROMACS timings and seeing where runs spend their time. diff -y -W 160<br>
can be useful here. Look at the MPMD flowchart in the manual (Figure<br>
3.15) to get an idea which parts match up with what lines.<br>
<br>
Speak with your admins and learn what you can. You might be able to<br>
mitigate the effects by using fewer processors, so that your<br>
computation/communication ratio goes up. Your throughput is lower, but<br>
your efficiency is higher. Or beg for dedicated network space to see<br>
what quiet-conditions performance looks like.<br>
<br>
> Here is the performance (in ns/day) that I obtain with a single run.<br>
> This is representative of what I see with 30 other runs (see list<br>
> below). First, the distribution is bimodal, with peaks at around 80<br>
> and 90 ns/day. Second, the values go as low as 70 ns/day (and I have<br>
> seen as low as 50 ns/day when I look through all 30 run directories<br>
> that differ only by the position of the umbrella restraint).<br>
><br>
> I am using gromacs 4.5.3 and I run it like this:<br>
> mpirun mdrun_mpi -deffnm md1 -dlb yes -npme 16 -cpt 30 -maxh 47 -cpi<br>
> md1.cpt -cpo md1.cpt -px coord.xvg -pf force.xvg -noappend<br>
><br>
> I have obtained similar behaviour also with another system.<br>
><br>
> I have attempted to correlate timing with the node on which the job<br>
> runs, the output of the "^Grid:" in the .log file, the DD division of<br>
> PME and real-space and the value of pme mesh/force, all to no avail. I<br>
> have found one correlation whereby the very slow runs also indicate a<br>
> high relative load for PME.<br>
<br>
That is suggestive of network noise - PME requires global<br>
intra-simulation communication.<br>
<br>
> I suspect that it is some value that is being determined at run start<br>
> time that is affecting my performance, but I am not sure what this<br>
> could be. Perhaps the fourier-spacing is leading to different initial<br>
> grids?<br>
<br>
I don't think "optimize_fft = yes" does much any more - but you can<br>
verify that by inspection of the start of the log file.<br>
<br>
Mark<br>
<br>
> Thank you (timing information and my .mdp file follows),<br>
> Chris<br>
><br>
> ########### Output the ns/day obtained by the run segments<br>
> $ grep Perf *log|awk '{print $4}'<br>
><br>
> 78.286<br>
> 82.345<br>
> 81.573<br>
> 83.418<br>
> 92.423<br>
> 90.863<br>
> 85.833<br>
> 91.131<br>
> 91.820<br>
> 71.246<br>
> 76.844<br>
> 91.805<br>
> 92.037<br>
> 85.702<br>
> 92.251<br>
> 89.706<br>
> 88.590<br>
> 89.381<br>
> 90.446<br>
> 81.142<br>
> 76.365<br>
> 76.968<br>
> 76.037<br>
> 79.286<br>
> 79.895<br>
> 79.047<br>
> 78.273<br>
> 79.406<br>
> 78.018<br>
> 78.645<br>
> 78.172<br>
> 80.255<br>
> 81.032<br>
> 81.047<br>
> 77.414<br>
> 78.414<br>
> 80.167<br>
> 79.278<br>
> 80.892<br>
> 82.796<br>
> 81.300<br>
> 77.392<br>
> 71.350<br>
> 73.134<br>
> 76.519<br>
> 75.879<br>
> 80.684<br>
> 81.076<br>
> 87.821<br>
> 90.064<br>
> 88.409<br>
> 80.803<br>
> 88.435<br>
><br>
> ########### My .mdp file<br>
><br>
> constraints = all-bonds<br>
> lincs-iter = 1<br>
> lincs-order = 6<br>
> constraint_algorithm = lincs<br>
> integrator = sd<br>
> dt = 0.004<br>
> tinit = 1000000<br>
> init_step = 0<br>
> nsteps = 1000000000<br>
> nstcomm = 1<br>
> nstxout = 1000000000<br>
> nstvout = 1000000000<br>
> nstfout = 1000000000<br>
> nstxtcout = 25000<br>
> nstenergy = 25000<br>
> nstlist = 5<br>
> nstlog=0 ; reduce log file size<br>
> ns_type = grid<br>
> rlist = 1<br>
> rcoulomb = 1<br>
> rvdw = 1<br>
> coulombtype = PME<br>
> ewald-rtol = 1e-5<br>
> optimize_fft = yes<br>
> fourierspacing = 0.12<br>
> fourier_nx = 0<br>
> fourier_ny = 0<br>
> fourier_nz = 0<br>
> pme_order = 4<br>
> tc_grps = System<br>
> tau_t = 1.0<br>
> ld_seed = -1<br>
> ref_t = 300<br>
> gen_temp = 300<br>
> gen_vel = yes<br>
> unconstrained_start = no<br>
> gen_seed = -1<br>
> Pcoupl = berendsen<br>
> pcoupltype = semiisotropic<br>
> tau_p = 4 4<br>
> compressibility = 4.5e-5 4.5e-5<br>
> ref_p = 1.0 1.0<br>
><br>
> ; COM PULLING<br>
> pull = umbrella<br>
> pull_geometry = position<br>
> pull_dim = N N Y<br>
> pull_start = no<br>
> pull_nstxout = 250<br>
> pull_nstfout = 250<br>
> pull_ngroups = 1<br>
> pull_group0 = POPC<br>
> pull_pbcatom0 = 338<br>
> pull_group1 = KSC<br>
> pull_pbcatom1 = 0<br>
> pull_init1 = 0 0 0.0<br>
> pull_rate1 = 0<br>
> pull_k1 = 3000.0<br>
> pull_vec1 = 0 0 0<br>
> ;;;EOF<br>
><br>
><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Wed, 22 Jun 2011 22:52:45 +0530<br>
From: Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>><br>
Subject: [gmx-users] Trajectory and ED - (not old question again)<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:BANLkTimMmZQcuAexfGbs_veFtg5s61qc0w@mail.gmail.com">BANLkTimMmZQcuAexfGbs_veFtg5s61qc0w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear users,<br>
<br>
I did ED analysis for one of the trajectories,<br>
when I visualised the trajectory along the first<br>
five eigen vectors using g_nmtraj it does not<br>
show much movements. It was a simulation of<br>
100 ns.<br>
My doubt is when I visualise the trajectory in<br>
pymol calculated just after simulation I could<br>
observe large movements in certain regions.<br>
same regions do have movements in ED<br>
trajectory also but not as large as this.<br>
Why is this?<br>
<br>
Thank you<br>
With Regards<br>
M. Kavyashree<br>
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Message: 5<br>
Date: Wed, 22 Jun 2011 17:48:28 -0400<br>
From: Ye Yang <<a href="mailto:knightyangpku@gmail.com">knightyangpku@gmail.com</a>><br>
Subject: [gmx-users]Question about reduced unit for coarse grain<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTimxfqVMT9ha9sHE=+<a href="mailto:ANKEfwAQSrPQ@mail.gmail.com">ANKEfwAQSrPQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear all:<br>
I see from the user's manual that if our input is in reduced unit,<br>
the output will also be in reduced unit(,<br>
<a href="ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf" target="_blank">ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf</a>), P25. On the<br>
contrary, if we use standard unit, the out put will be in standard unit.<br>
This brings the question up when we use coarse grain Clementi's<br>
model webtool (<a href="http://smog.ucsd.edu/sbm_faq.html" target="_blank">http://smog.ucsd.edu/sbm_faq.html</a>), according to the author,<br>
it seems that everything is in reduced unit, so the output file should also<br>
be in reduced unit, yet I found the topology file that the energy unit is<br>
KJ/mol. What exactly is the unit of the input and out put file? When I pull<br>
the molecules, do I get the reduced unit result or the physical unit result?<br>
Since I am an experimentalist, getting the physical units is more<br>
important to me, so as to compare with the experimental results, albeit the<br>
intrinsic difference. If I get something in reduced unit, there is necessity<br>
for me to change it into physical unit, or at least clarify it in<br>
comparison.<br>
Thank you very much.<br>
<br>
Ye<br>
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Message: 6<br>
Date: Wed, 22 Jun 2011 18:15:51 -0400<br>
From: Zack Scholl <<a href="mailto:zns@duke.edu">zns@duke.edu</a>><br>
Subject: [gmx-users] Relaxed frozen groups<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:BANLkTimrMdP_hxJLMetFhQscgi4fJqsX0w@mail.gmail.com">BANLkTimrMdP_hxJLMetFhQscgi4fJqsX0w@mail.gmail.com</a>><br>
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<br>
Hi all-<br>
<br>
Is it possible to freeze a group of atoms only partially in a<br>
direction? For instance, could I freeze a group inside a box of a<br>
definite size?<br>
<br>
<br>
Sincere thanks,<br>
<br>
Zack<br>
<br>
<br>
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End of gmx-users Digest, Vol 86, Issue 143<br>
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