Dear All,
I believe I saw this Amber9 bug too; and even informed someone
about it back in spring if I recall correctly.
Have a great day,
Volodymyr
On Thu, September 11, 2008 11:59, David A. Case wrote:
> On Wed, Sep 10, 2008, Holger Gohlke wrote:
>>
>> I sent the email below yesterday, but I am not sure whether it went
>> through on the amber-developers reflector. If I am right, the problem
>> that
>> we found is severe, because restarting a REMD run would mean to take the
>> wrong coordinates for the respective temperature. I attached a patch and
>> I
>> would be happy if you can have a look here.
>
> I'll forward this to the developers' list, since it doesnt' seem to be
> on the archives.
>
>>
>> Finally, may I ask to get CVS access again to the amber tree? Currently,
>> we are correcting some overdue issues related to mm_pbsa, and we would
>> like to carry over the changes to amber11.
>
> I'll look into this and get back to you.
>
> ...dave
>
>>
>> ------------------------ Ursprüngliche Nachricht
>> -------------------------
>> Betreff: input coords for REMD in Amber9
>> Von: "Holger Gohlke" <gohlke.pharmazie.uni-kiel.de>
>> Datum: Di, 9.09.2008, 15:55
>> An: amber-developers.scripps.edu
>> --------------------------------------------------------------------------
>>
>> Dear all,
>>
>> I think we ran across a problem when restarting a REMD run in Amber 9
>> using REPCRD=0. In this case, the wrong input coordinates for the
>> anticipated temperature are read. This is shown in the REMD debug
>> information below.
>>
>> I attach a patch file that should correct this, but I would be happy if
>> somebody can confirm this.
>>
>> Best regards
>>
>> Holger
>>
>> >>>>>
>> calling sander to get initial energy
>>
>> in runmd, myeptot is -3660.81356490524
>> in runmd, mytargettemp is 300.000000000000
>>
>> back from first sander call
>> MyEptot is -3660.81356490524
>> MAIN LOOP, currx is 1
>> calling subrem on exchange # 1
>> gathering temperature/energy data
>> doing myindex lookup
>> mytargettemp is 300.000000000000
>> temptable
>> 300.000000000000 305.811500000000 311.735300000000
>> 317.773400000000 323.928100000000 330.201600000000
>> 336.596300000000 343.114400000000 349.758400000000
>> 356.530600000000 363.433600000000 370.469900000000
>> 377.642000000000 384.952600000000 392.404400000000
>> 400.000000000000
>> my index in sorted T list: 1
>> my replica # is 9
>> l_index and r_index are 16 2
>> l_temp0 and r_temp0 are 400.000000000000 305.811500000000
>> l_repnum and r_repnum are 16 2
>> jumpright is T
>> partner index 16
>> partner repnum 16
>> myeptot and o_eptot are -3660.81356490524 -2841.08902648973
>> mytemp and o_temp are 300.000000000000 400.000000000000
>> NOT controlling exchange
>> done with exchange swap
>> exchange is F
>> newtargettemp is 300.000000000000
>> leaving subrem
>> called mdfil to change file names
>> here is my post-exchange file info
>> mdin:
>> md_nvt_prod_impl_re_940.in.000
>>
>> mdout:
>> md_nvt_prod_impl_re_940.out.000
>>
>> mdcrd:
>> md_nvt_prod_impl_re_940.mdcrd.000
>>
>> mdinfo:
>> mdinfo
>>
>> inpcrd:
>> md_nvt_prod_impl_re_939.restrt.000
>> ^^^^^
>> !!! This should be 008 instead of 000, because at the end of run 939,
>> !!! it was replica 9 that had a target temperature of 300K.
>>
>> restrt:
>> md_nvt_prod_impl_re_940.restrt.008
>>
>> calling sander for MD run
>> >>>>>
>>
>>
>> --
>> ++++++++++++++++++++++++++++++++++++++++++++++++++
>> Dr. Holger Gohlke
>
Received on Fri Sep 12 2008 - 03:07:18 PDT
