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 - 03:07:11 PDT
