Re: [AMBER-Developers] [ FW: REMD with AMOEBA]

From: Niel Henriksen <>
Date: Tue, 1 May 2012 21:39:07 +0000

I just started doing some REMD with pmemd from Amber12.
I'm glad someone caught this.

I had been using ascii restarts ... I wasn't sure about the status of
netcdf restarts and they aren't mentioned in the manual.

Here is what I found:
- sander.MPI reads temps from the ascii restart correctly
- pmemd.MPI DOES NOT read temps from ascii restarts (they come from mdin)
- pmemd.MPI does read temps from netcdf restarts correctly

Also, the reported bugfix DOES fix the problem. I don't really understand
the history behind all the inpcrd formats being checked in inpcrd_dat.F90
but it must not be doing what we think it is.

Maybe someone else can comment from here.

Bottom line: BEWARE if using ascii restarts and REMD in pmemd.MPI


From: case []
Sent: Tuesday, May 01, 2012 10:01 AM
Subject: [AMBER-Developers] [ FW: REMD with AMOEBA]

The message below seems to relate to REMD inside pmemd. Any comments from
those involved with this? (Seems to relate to sander6 or pmemd 2.01(?)
formats.) I'm confused by the subject line, since I don't think(?)
there is support for REMD in pmemd.amoeba.


----- Forwarded message from "Ren, Pengyu" <> -----

From: "Ren, Pengyu" <>
To: case <>
Subject: FW: REMD with AMOEBA
Date: Tue, 1 May 2012 15:03:27 +0000

Robert Best suggests there is a bug in the (regular and AMOEBA) pmemd
inpcrd_dat.F90 which causes the temperature not to be read from the
restart file. It is the line 141 in the attached file. The addition of
"local_temp0" should fix this problem.

From: Robert Best <<>>
Date: Friday, April 27, 2012 2:54 AM
To: Pengyu Ren <<>>
Subject: Re: REMD with AMOEBA

In the amber development version it is just line 141 in inpcrd_dat.F90. I've attached the corrected file.

I assume everyone uses binary or netcdf restarts now so that's why it wasn't picked up?


Robert Best
Royal Society University Research Fellow
Department of Chemistry
Lensfield Road, Cambridge CB2 1EW
Tel: +44-(0)1223-336470 | Fax: +44-(0)1223-336362

> On 4/26/12 10:21 AM, "Robert Best" <<>> wrote:
>> I've uploaded a new pmemd with some bugfixes relating to reading
>> formatted restart files with REMD. Actually, this bug was present in the
>> standard PMEMD and I had just copied it over. The bug caused the
>> temperature not to be read from the restart file.
>> Another thing I noticed in your prmtop files is that in the
>> ATOMS_PER_MOLECULE section, the first hydrogen of ALA5 has been split
>> into a different molecule. I don't think this has any real effect on the
>> simulation, only the way that iwrap works. This was also causing problems
>> with the restarts, but is easy to fix by hand.
>> Robert

----- End forwarded message -----

David A. Case                     |
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