[gmx-users] R: Md continuation with cpt
Anna Marabotti
anna.marabotti at isa.cnr.it
Thu Apr 28 09:47:25 CEST 2011
Dear Justin,
thank you for your precious help. Yes, the problem is what you say and what
I was suspecting too (but I was not sure, that's why I was searching for a
confirmation of my suspects from more expert people). The problem however is
present in the NVT->NPT junction. My .mdp settings were
NVT:
tinit = 0
init_step = 0
nsteps = 10000
dt = 0.002
NPT
tinit = 0
init_step = 20000 (instead of 10000)
nsteps = 50000
dt = 0.002
That's why I had a last NPT step of 70000 instead of 60000, and that's why I
set init_step = 70000 in the production MD.
What you are saying also explains the anomalous behaviour of the xvg file
created from the .edr file, in which only few points were saved, therefore
the graphs created with xmgrace contain only 7 values (at 140, 200, 300 400,
5140, 10140, 15140 ps).
I always set nstep identical to the last step of the previous equilibration
MD because I understood that it was necessary to do it to obtain an exact
continuation, there is no other special reason. Since you are saying that
this is no (longer?) necessary (I'm currently using Gromacs 4.0.7 on this
machine), I'm very happy to set always nsteps = 0, to avoid future mistakes.
In the meantime, what I have to do? I had a look at the .xtc files with
gmxcheck and apparently all is fine, with no error messages, also the
trajectory seems to be coherent with my expectations. I run g_rms and
g_gyrate and the behaviour of the systems appears "normal" (apart from the
fact that the system is not stabilized yet, so I have to continue the
trajectory). I can provide you (offlist) the .xvg graphs, if you want.
Based on these data, what do you suggest to do? Do you think that the
simulation could be considered formally correct (i.e. this is only a problem
of erroneous writing of .edr file) or do I have to repeat
(AAAAAARRRRRRGGGGHHHHH) the whole simulation? I saw in the manual that the
option -rerun of mdrun command allows to recalculate forces and energies
from a trajectory file, do you think that I can use it to obtain a new .edr
file?
Thank you as usual for your invaluable help
Anna
PS: i'm asking just another suggestion, to the gmx-users administrators. I
receive the mails from gmx-users list in form of digest. How can I do to
reply to messages extracted from the digest in order to create a continuous
thread in the archive? At present, I'm making a reply to the digest message
in order to keep the gmx-users list updated, but it seems to me that the
messages are stored as separated.
----------------------------------------------------------------------
Message: 1
Date: Wed, 27 Apr 2011 11:18:51 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Md continuation with cpt
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DB833DB.4050902 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Anna Marabotti wrote:
> Dear gmx-users,
> since I'm sending my simulations to a system with a queue with a
> wallclock time of 24 h, I necessarily have to simulate small parts of my
> simulation, that I "stick" together at the end with trjconv. To continue
> my simulations, I'm using the .cpt file. Here my settings concerning the
> number of steps, dt etc. Since I started the full MD after 20 ps NVT and
> 100 ps NPT I set the mdp file as:
>
> integrator = md
> dt = 0.002
> nsteps = 2500000 (total 5 ns - the max time compatible with the
> wallclock time)
> init_step = 70000 (the last step after NVT+NPT)
Is it? 120 ps/0.002 ps = 60000 steps.
<snip>
> Opened 1R3Afull20ns.edr as double precision energy file
> frame: 0 (index 0), t: 140.000
Based on this output, frame 0 corresponds to a time of 140 ps, as set by
your
init_step * dt.
> Reading energy frame 2 time 300.000
> Timesteps at t=200 don't match (60, 100)
It looks like the setting for nstenergy is causing frames to be written at
integral multiples of 100 ps, rather than init_step + nstenergy. So you
have
frame 0 at 140 ps, frame 1 at 200 ps, then 100-ps intervals until...
> Reading energy frame 50 time 5100.000
> Timesteps at t=5100 don't match (100, 40)
>
etc.
> Timesteps at t=5140 don't match (40, 60)
>
> Timesteps at t=5200 don't match (60, 100)
> Reading energy frame 100 time 10000.000
> Timesteps at t=10100 don't match (100, 40)
>
> Timesteps at t=10140 don't match (40, 60)
>
> Timesteps at t=10200 don't match (60, 100)
> Reading energy frame 150 time 14900.000
> Timesteps at t=15100 don't match (100, 40)
>
> Timesteps at t=15140 don't match (40, 60)
>
> Timesteps at t=15200 don't match (60, 100)
> Last energy frame read 198 time 19600.000
>
All of these mismatches seem to agree with the above theory. The difference
is
always 40 or 60, the remainder of some break between your value determined
by
init_step and initial time of 140 ps.
> Found 199 frames.
>
> gcq#131: "Royale With Cheese" (Pulp Fiction)
> I don't understand why there are so many mismatches in my file. Moreover
> all but one are in the correspondence of the "junctions" I made between
> two consecutive 5 ns runs. Does it depend on some settings regarding
> init_step or dt or tinit in the .mdp file? Did I make correctly the
> continuation? Could somebody help me to find the error?
Is there some reason you needed the trajectory to start at 140 (120?) ps?
Usually a new trajectory is intitiated with init_step = 0. Continuing a run
using while still maintaining the previous ensemble does not necessarily
need
init_step > 0.
It is possible this is a bug related to nst*out/energy/log being writing
every
50000 steps and assuming init_step = 0 (i.e. writing at 100 ps rather than
240
ps, based on your initial settings). What version of Gromacs is this?
-Justin
> Many thanks in advance and best regards
> Anna
>
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
>
> "When a man with a gun meets a man with a pen, the man with the gun is a
> dead man"
> (Roberto Benigni, about Roberto Saviano)
>
>
--
========================================
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, 27 Apr 2011 11:21:19 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Md continuation with cpt
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4DB8346F.8030900 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Justin A. Lemkul wrote:
> It is possible this is a bug related to nst*out/energy/log being writing
> every 50000 steps and assuming init_step = 0 (i.e. writing at 100 ps
> rather than 240 ps, based on your initial settings). What version of
> Gromacs is this?
Actually, this wouldn't be considered a bug. If you're telling grompp that
you've done 70000 steps previously, the input will then expect that these
frames
exist, and the output is always written every nst*out/energy/log steps.
Thus,
all intervals of the concatenated trajectory or energy files should have
consistently spaced frames. In your case, this is not true.
-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
========================================
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