# Re: [AMBER] Consistency between temperatures in mdout and mdcrd in REMD

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 11 Feb 2011 13:57:49 -0500

Hi Dan,

On Fri, Feb 11, 2011 at 5:08 AM, Daniel Sindhikara <sindhikara.gmail.com> wrote:
> According to this, the rem.log and mdcrds are consistent, but the mdout does
> not follow the same "replica series"

I also see this behavior to a certain extent:

\$ grep TEMP0 OUTPUT/rem.out.004 | head
TEMP0 = 491.6000 REPNUM = 5 EXCHANGE# = 1
TEMP0 = 491.6000 REPNUM = 5 EXCHANGE# = 2
TEMP0 = 491.6000 REPNUM = 5 EXCHANGE# = 3
TEMP0 = 445.4000 REPNUM = 5 EXCHANGE# = 4
TEMP0 = 445.4000 REPNUM = 5 EXCHANGE# = 5
TEMP0 = 445.4000 REPNUM = 5 EXCHANGE# = 6
TEMP0 = 403.5000 REPNUM = 5 EXCHANGE# = 7
TEMP0 = 365.5000 REPNUM = 5 EXCHANGE# = 8
TEMP0 = 331.2000 REPNUM = 5 EXCHANGE# = 9
TEMP0 = 331.2000 REPNUM = 5 EXCHANGE# = 10
\$ grep REMD TRAJ/rem.crd.004 | head
REMD 5 1 500 542.700
REMD 5 2 1000 491.600
REMD 5 3 1500 491.600
REMD 5 4 2000 491.600
REMD 5 5 2500 445.400
REMD 5 6 3000 445.400
REMD 5 7 3500 445.400
REMD 5 8 4000 403.500
REMD 5 9 4500 365.500
REMD 5 10 5000 331.200
\$ awk -v rep=4 '{if (4==(rep+1)) print ;}' rem.log | head
542.70
491.60
491.60
491.60
445.40
445.40
445.40
403.50
365.50
331.20

However in my case the temperature in my mdout is shifted by -1 (so
the temp0 written for exchange 1 in mdout is really the temp0 for
exchange 2 in rem.log). The temp0 in rem.log and mdout is the actual
thermostat temperature of the replica at the time of exchange. After
exchanging temp0 gets set to the new bath temperature and so by the
time we hit the prntmd() call in runmd, temp0 is the temperature after
the exchange. So the temps in the rem.log and mdcrd files should be
OK. The exchange/temp0 information in mdout is a little misleading in
I'm not even sure this info is worth printing to mdout, but maybe it
should be labelled NewTemp0 instead of Temp0 or something.

In your case you're writing every 10 exchanges, so the offset isn't as
apparent. Check and see if the Temp0 info in mdout matches the
NewTemp0 column of the rem log. If not, let me know - then there may
be bigger issues.

-Dan

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Received on Fri Feb 11 2011 - 11:00:02 PST
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