[namd] Help with sortreplicas

From: Canal de Sebassen (thecromicusproductions_at_gmail.com)
Date: Sat Mar 09 2019 - 13:01:49 CST

Hi everyone,

How are y'all doing? I hope that great! I'm trying to analyze some REUS
simulation results. I ran 25 replicas with the following parameters:
     set steps_per_run 1000
     set num_runs 500
     set runs_per_frame 10
     set frames_per_restart 5
And when I run
     sortreplicas %d/AmtB-A.job0 25 10
I get sorted dcd files much smaller than the original ones. The sorted
history and colvar files are more or less of the same size than the
original ones. Is this normal or will it affect my results?

Also, I performed three different runs with different durations
     sortreplicas %d/AmtB-A.job0 25 10
     sortreplicas %d/AmtB-A.job1 25 10
     sortreplicas %d/AmtB-A.job2 25 10

If I want to get the PMF using WHAM, what I was currently doing was
cocatenating the sorted colvar files and running an input file INPUT1
through
./wham/./wham -6 160 50 0.0001 295.0 0 INPUT1 AmtB_REMD_US_0.1-0.626ns.pmf
where the input file is:

## wham -6 160 50 0.0001 295.0 0 INPUT1 AmtB_REMD_US_0.1-0.626ns.pmf
##/path/to/timeseries/file loc_win_min spring [correl time] [temp]
##
SORTEDCOLVARS/file.0.sort.colvars.traj 160.0 0.1
SORTEDCOLVARS/file.1.sort.colvars.traj 153.4 0.1
SORTEDCOLVARS/file.2.sort.colvars.traj 146.8 0.1
SORTEDCOLVARS/file.3.sort.colvars.traj 140.2 0.1
SORTEDCOLVARS/file.4.sort.colvars.traj 133.6 0.1
SORTEDCOLVARS/file.5.sort.colvars.traj 127.0 0.1
SORTEDCOLVARS/file.6.sort.colvars.traj 120.4 0.1
SORTEDCOLVARS/file.7.sort.colvars.traj 113.80000000000001 0.1
SORTEDCOLVARS/file.8.sort.colvars.traj 107.2 0.1
SORTEDCOLVARS/file.9.sort.colvars.traj 100.6 0.1
SORTEDCOLVARS/file.10.sort.colvars.traj 94.0 0.1
SORTEDCOLVARS/file.11.sort.colvars.traj 87.4 0.1
SORTEDCOLVARS/file.12.sort.colvars.traj 80.80000000000001 0.1
SORTEDCOLVARS/file.13.sort.colvars.traj 74.2 0.1
SORTEDCOLVARS/file.14.sort.colvars.traj 67.60000000000001 0.1
SORTEDCOLVARS/file.15.sort.colvars.traj 61.0 0.1
SORTEDCOLVARS/file.16.sort.colvars.traj 54.400000000000006 0.1
SORTEDCOLVARS/file.17.sort.colvars.traj 47.80000000000001 0.1
SORTEDCOLVARS/file.18.sort.colvars.traj 41.2 0.1
SORTEDCOLVARS/file.19.sort.colvars.traj 34.60000000000001 0.1
SORTEDCOLVARS/file.20.sort.colvars.traj 28.0 0.1
SORTEDCOLVARS/file.21.sort.colvars.traj 21.400000000000006 0.1
SORTEDCOLVARS/file.22.sort.colvars.traj 14.800000000000011 0.1
SORTEDCOLVARS/file.23.sort.colvars.traj 8.200000000000017 0.1
SORTEDCOLVARS/file.24.sort.colvars.traj 1.6000000000000227 0.1

Is this OK? I obtained linear and very high free energy profiles and I'm
trying to find out what could I be doing wrong.

Thanks a lot,

Sebastian

This archive was generated by hypermail 2.1.6 : Sat Sep 21 2019 - 23:20:16 CDT