Re: restarting Gaussian accelerated MD fails

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Fri Jan 25 2019 - 04:11:03 CST

Thanks Yinglong, Andrew for the explanation ...

The restart problem is still there. The restart file is not read
properly (namd log says at first time step that dV = 0, iE = 0, k0 = 0)
and the simulation crashes soon after that although NAMD does recognize
the restart file as input ("accelMDG USING RESTART FILE
oct4_hoxb1_mur_01_box_gamd010102.gamd" ) ... The restart file also seems
correct.

Curiously that it appears that nobody else has encountered this issue ....

I guess I will wait for David's feed back ... He has all files needed to
reproduce the issue ..
I provide below again the relevant input lines and the restart file ... 
Maybe somebody sees something obvious that I am missing ....

Vlad

---- NAMD input -----
#*** Accelerated MD
**********************************************************************************
accelMD                                       on
accelMDG                                      on
accelMDdihe                                   on
accelMDdual                                   on
accelMDFirstStep                        25000000
accelMDLastStep                         50000000
accelMDOutFreq                              2500

accelMDGiE                                     1
accelMDGcMDPrepSteps                           0
accelMDGcMDSteps                               0
accelMDGEquiPrepSteps                          0
accelMDGEquiSteps                              0
accelMDGSigma0P                                6
accelMDGSigma0D                                6
accelMDGRestart                               on
accelMDGRestartFile               test.gamd

---------- GAMD restart  (test.gamd) --------
# NAMD accelMDG restart file
# D/T Vn Vmax Vmin Vavg sigmaV M2 E k
D 10000000 4779.3504030500444 4469.4517421030359 4633.215337071334
49.785203930094141 2.47856653036106071e+10 4779.3504030500444
0.0008247009977261319
T 10000000 -974348.98058993137 -984746.7871256324 -976797.22733897553
856.08499832075404 7.32881524349845312e+12 -974348.98058993137
2.8627220105560853e-06

On 1/24/19 2:02 AM, Pang Andrew wrote:
>
> Dear Vlad,
>
> Dr Miao is right. The second column of the restart file shows the
> number of steps used to obtain the statistics instead of the number of
> simulation steps.
>
> Sincerely,
>
> Andrew
>
> On Tue, Jan 22, 2019, 3:10 PM Miao, Yinglong <miao_at_ku.edu
> <mailto:miao_at_ku.edu> wrote:
>
>
>
> On Jan 22, 2019, at 2:56 AM, Vlad Cojocaru
> <vlad.cojocaru_at_mpi-muenster.mpg.de
> <mailto:vlad.cojocaru_at_mpi-muenster.mpg.de>> wrote:
>
> I also have a question regarding the k0 values. During the
> gAMD equilibration, these values are updated at each time step
> whereas during a production run , k0 is maintained constant
> throughout the simulation ...  That is correct, right ?
>
> Dear Vlad,
>
> Yes, k0 works in the way as you described.
>
> Hope David can help with the simulation restart problem, and
> Andrew on the step number in the restart file (Should it be the
> number used to calculate average and standard deviation of the
> boost potential?)
>
> Best wishes,
>
> Yinglong
>
> Yinglong Miao, Ph.D.
> Assistant Professor
> Center for Computational Biology and
> Department of Molecular Biosciences
> University of Kansas
> http://miao.compbio.ku.edu
>

-- 
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru

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