this could be related to a problem I've been working on. if possible, check
the restraint energies at the start of the run (try a much shorter run,
maybe nstlim=10, and set ntpr=1). also try using iwrap=0 in all of the
relaxation runs; with a complex the wrapping can cause serious problems on
restarting with restraints.
On Mon, Sep 7, 2026 at 7:43 AM Iglika Lessigiarska via AMBER <
amber.ambermd.org> wrote:
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> Dear Amber Community
>
> I have the following situation:
>
> I heat my system (enzyme-ligand complex with water solvent) up to 310 K
> keeping the enzyme-lignad coordinates fixed, and then I start
> equilibrating the pressure with the following settings:
>
> &cntrl
> imin=0,
> irest=1, ntx=5,
> ig=-1,
> ntt=3, tempi=310.0, temp0=310.0, gamma_ln=2.0,
> ntp=1, pres0=1.0, taup=0.1, barostat=1,
> ntb=2,
> cut=10.0,
> ntc=2, ntf=2,
> vlimit=20,
> ntr=1, restraint_wt=2.0, restraintmask=':1-266',
> nstlim=10000000, dt = 0.001,
> ntwx=100000, ntpr=1000, ntwr=10000000, ntwe=0, ntave=10000000,
> /
>
> During the first pressure-equilibration run the temperature/pressure are
> correct, but if I run the system from the restart file of this run with
> the same settings (i.e. like restarting the same run), in the first 1-2 ps
> the temperature raises up to 330-370 K, and then it goes back again to 310
> K.
> This happened to me with two different enzyme-ligand systems.
>
> Please let me know why this temperature elevation happens and how to avoid
> it.
>
> Thank you in advance
> Best regards
> Iglika
>
> --
> Iglika Lessigiarska, PhD
> Department of QSAR and Molecular Modelling
> Institute of Biophysics and Biomedical Engineering
> Bulgarian Academy of Sciences
> Acad. G. Bonchev Str, Bl. 105
> 1113 Sofia, BULGARIA
> e-mail: iglika.biomed.bas.bg
>
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Received on Wed Sep 09 2026 - 11:00:06 PDT
