Dear Amber users
I’ve just started running pH replica exchange with Amber 16, but I have problems with the reconstruction of the trajectory files.
This is my cpptraj script when I’m trying to extract data for pH 4.5:
#!/bin/bash
parm new_radii_prmtop
trajin mdcrd.pH.000 remdtraj remdtrajtemp 4.5
trajout fixed.mdcrd.4.5
go
And this is what I get when I try to run it:
CPPTRAJ: Trajectory Analysis. V16.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 03/15/17 11:20:23
| Available memory: 154.980 MB
INPUT: Reading input from 'reconstructing_traj.cpptraj'
[parm new_radii_prmtop]
Reading 'new_radii_prmtop' as Amber Topology
[trajin mdcrd.pH.000 remdtraj remdtrajtemp 4.5]
Found 8 replicas.
Reading 'mdcrd.pH.000' as Amber NetCDF
[trajout fixed.mdcrd.4.5]
Warning: Format not specified and extension '.5' not recognized. Defaulting to Amber Trajectory.
Writing 'fixed.mdcrd.4.5' as Amber Trajectory
[go]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: new_radii_prmtop, 39702 atoms, 12475 res, box: Orthogonal, 12289 mol, 12275 solvent
INPUT TRAJECTORIES (1 total):
0: REMD trajectories (8 total), lowest replica 'mdcrd.pH.000' (reading 5000 of 5000)
Looking for frames at 4.50 K
Coordinate processing will occur on 5000 frames.
OUTPUT TRAJECTORIES (1 total):
'fixed.mdcrd.4.5' (5000 frames) is an AMBER trajectory
BEGIN TRAJECTORY PROCESSING:
----- mdcrd.pH.000 (1-5000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 5000 frames and processed 5000 frames.
TIME: Avg. throughput= 15.3555 frames / second.
ACTION OUTPUT:
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 325.6154 s ( 99.88%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0017 s ( 0.00%)
TIME: Other : 0.3804 s ( 0.00%)
TIME: Run Total 325.9976 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 326.1784 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
To me it seems like it is not able to read all my files, but I am quite new to this so I haven’t been able to figure out how to fixed it myself.
This is the input I’ve used when running the jobs, with changing the solvph from 4.0 to 7.5:
prod 2bem
&cntrl
ig=-1
iwrap =1
imin=0,irest=1,ntx=5,
nstlim=1000,dt=0.002,
numexchg=50000,
ntc=2,ntf=2,
cut=12, ntb=1, ntp=0, tautp=10.0,
ntpr=1000, ntwx=10000, ntwr=10000,
ntt=1,
temp0=300.0,
tol=1.0e-8,jfastw=0,
ntr=1, restraintmask = ':1,108,172 & !.H=',
restraint_wt=1.0,
saltcon=0.1, icnstph=2, ntcnstph=100, ntrelax=200,
solvph=4.5,
/
&ewald
dsum_tol=1.0e-6,
order=4, skinnb=2.0, vdwmeth=1,
/
I’ve checked the replica exchange log file and to me it looks like the pH swaps are going well, it look like the ones I’ve found in tutorials.
I hope someone can help me with what I am doing wrong.
Thanks in advance for all help!
Best regards,
Ingvild Isaksen
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Received on Wed Mar 15 2017 - 05:30:03 PDT
