Re: AMBER: pmemd iwrap trouble

From: Robert Duke <>
Date: Mon, 25 Aug 2008 08:40:03 -0400

Hi Lars,
I am on vacation today, but will look at it tomorrow. There should not be a
problem with wrapping in amber 10 pmemd; there was a bug in amber 9 pmemd
for which a patch was released. That said, I am not sure there is not some
intricacy when binary trajectory files are in use, and I will have to look.
It should not matter, as the restart file is the primary issue here, and it
is not binary, but maybe there is some combination of inputs that screws up
on wrapping. Are you sure it is not just an imaging problem? I have grief
going back and forth between what pmemd or sander does and what ptraj does
(but I am talking constant pressure here, and ptraj I think hits grief with
the changing boxsize). Anyway, I will look into it, but you might try a 1
step, no binary output run just for grins, or do a single step in sander and
see if you get the same result (just gives me more info, in case something
obvious does not jump out).
Thanks - Bob Duke

----- Original Message -----
From: "Lars Skjærven" <>
To: <>
Sent: Monday, August 25, 2008 6:25 AM
Subject: AMBER: pmemd iwrap trouble

> Dear Amber users,
> I've been running a MD-simulation for about 40ns and needed to wrap
> the water back into the primary box (due to water has swimed too far
> away). As recommended on the mailinglist I used iwrap for only one
> step:
> Wrap it
> &cntrl
> imin= 0, irest= 1, ntx = 5,
> ntb = 1,
> cut = 10,
> ntc = 2, ntf = 2, tol = 0.000001,
> ntt = 0,
> nstlim = 1, dt = 0.001,
> ntpr = 1, ntwx = 1, ntwr = 5,
> ioutfm = 1, iwrap = 1,
> &ewald
> dsum_tol = 0.000001,
> /
> The restart file produced by this run has about 50% of the solute
> outside the waterbox (when visualized in vmd). I can still carry on my
> MD-runs (with iwrap=0) after this, but I am worried about the new
> coordinates for the solute with respect the the water.
> However, when I do reimage in ptraj it seems to be ok:
> center :1-224
> image familiar
> trajout test.rst restart
> It must be said I use an octahedral water box. Both pmemd9 and 10
> yields the same results for me with this respect.
> To wrap it up:
> - should iwrap=1 with pmemd10 work when using a octahedral box ?
> - or should I use ptraj to reimage? if so, are the velocities ok ?
> I realise this is a topic that has been discussed on the mailinglist
> earlier and I apologise if my questions are redundant. I searched, but
> did not find a clear answer on this..
> Best regards,
> Lars Skjaerven
> University of Bergen, Norway
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Received on Wed Aug 27 2008 - 06:07:25 PDT
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