Dear sir,
I wish to seek some help for calculating rotational diffusion for a small portion of my lipid in a lipid bilayer.
My simulation system:
I have a lipid bilayer containing 256 lipids in four layers. (Each layer contains 64 lipids). My single lipid is have two sugar rings - connected to alkyl chain. In total I have 40,000 frames. The time difference between two frames is 5ps.
What I want:
Basically I want to calculate the time taken by each ring from lipids to make rotational diffusion. In other words, I wish to calculate the rotational diffusion of (first frame-first lipid-first sugar ring) until the (40,000th frame-first lipid-first sugar ring). I want to do the same for the second ring. Later I want to compare their relative times.
My residue name is DDM. I defined the vector of rotation C21 to C24. This is actually vector from C1-C4 of a sugar in the chair conformation.
To achieve this, I would like to use the cpptraj tool. As for a test I tried to work with 1000 frames. The command I used is:
path="/home/vijay/Simulation-Folder-Feb2013/chapter5-thermo-paper2-Vj/maltoThermo"
cpptraj thermoMalto.top << EOF
reference $path/thermoMalto-reimage-set1.traj.pdb.1 [avg]
trajin $path/thermoMalto-reimage-set1.traj 1 1000
rotdif nvecs 1000 ref [avg] :1.C21, C24 \
ncorr 500 ti 0.0 tf 1 dt 0.001 deffout deffs.dat \
itmax 100 tol 0.000001 d0 0.03 order 2 \
outfile rotdif.out
EOF
note: thermoMalto-reimage-set1.traj.pdb.1 is the first pdb frame from the production stage.
When I tried to run this, I get error message as below:
CPPTRAJ: Trajectory Analysis. V13.15
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
INPUT: Reading Input from STDIN
[reference /home/vijay/Simulation-Folder-Feb2013/chapter5-thermo-paper2-Vj/maltoThermo/thermoMalto-reimage-set1.traj.pdb.1 [avg] ]
[thermoMalto-reimage-set1.traj.pdb.1] contains 1 frames.
[thermoMalto-reimage-set1.traj.pdb.1] is a PDB file, Parm thermoMalto.top (reading 1 of 1)
[trajin /home/vijay/Simulation-Folder-Feb2013/chapter5-thermo-paper2-Vj/maltoThermo/thermoMalto-reimage-set1.traj 1 1000 ]
[thermoMalto-reimage-set1.traj] contains 1000 frames.
[rotdif nvecs 1000 ref [avg] :1.C21, C24 ncorr 500 ti 0.0 tf 1 dt 0.001 deffout deffs.dat itmax 100 tol 0.000001 d0 0.03 order 2 outfile rotdif.out]
ROTDIF: Random seed 80531, # of random vectors to generate: 1000
Max length to compute time correlation functions: 500
Timestep = 0.0010, T0 = 0.0000, TF = 1.0000
Vector correlation functions will be calculated directly
Iterative solver: Max iterations = 100, tol = 0.000001, initial guess = 0.030000
Order of Legendre polynomial = 2
Simplex scaling factor=0.5000
Deff will be written out to deffs.dat
Diffusion constants and tau will be written to rotdif.out
Warning: [rotdif] Not all arguments handled: [ C24 ]
PARAMETER FILES:
0: thermoMalto.top, 20736 atoms, 256 res, box: Orthogonal, 256 mol, 1000 frames
INPUT TRAJECTORIES:
0: [thermoMalto-reimage-set1.traj] is an AMBER trajectory, Parm thermoMalto.top (Orthogonal box) (reading 1000 of 1000)
Coordinate processing will occur on 1000 frames.
REFERENCE COORDS:
The following 1 frames have been defined:
0: [avg] frame 1
Active reference frame for masks is 0
OUTPUT TRAJECTORIES:
No files.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM [thermoMalto.top] (1 actions):
0: [rotdif nvecs 1000 ref [avg] :1.C21, C24 ncorr 500 ti 0.0 tf 1 dt 0.001 deffout deffs.dat itmax 100 tol 0.000001 d0 0.03 order 2 outfile rotdif.out]
ROTDIF: 1 atoms selected for RMS fit.
----- [thermoMalto-reimage-set1.traj] (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 1000 frames and processed 1000 frames.
ACTION OUTPUT:
ROTDIF:
1000 vectors, 1000 rotation matrices.
Determining local diffusion constants for each vector.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% The algorithm computing the eigenvalues/eigenvectors of D failed to converge.
100% Complete.
Determining diffusion tensor with small anisotropy.
Determining diffusion tensor with full anisotropy.
Max iterations (10000) exceeded in amoeba.
DATASETS:
No data sets.
./script_run_rotdiff.sh: line 16: 16834 Aborted cpptraj thermoMalto.top <<EOF
reference $path/thermoMalto-reimage-set1.traj.pdb.1 [avg]
trajin $path/thermoMalto-reimage-set1.traj 1 1000
rotdif nvecs 1000 ref [avg] :1.C21, C24 ncorr 500 ti 0.0 tf 1 dt 0.001 deffout deffs.dat itmax 100 tol 0.000001 d0 0.03 order 2 outfile rotdif.out
EOF
*** glibc detected *** cpptraj: double free or corruption (!prev): 0x0000000002405cb0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7ae56)[0x7f35c12a7e56]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f35c12ac13c]
cpptraj[0x471520]
cpptraj[0x4718c9]
cpptraj[0x48d88e]
cpptraj[0x4cba5e]
cpptraj[0x40aeec]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f35c124e30d]
cpptraj[0x40af45]
======= Memory map: ========
00400000-0062e000 r-xp 00000000 08:02 3178782 /usr/local/apps/amber12/bin/cpptraj
0082d000-0082e000 r--p 0022d000 08:02 3178782 /usr/local/apps/amber12/bin/cpptraj
0082e000-00836000 rw-p 0022e000 08:02 3178782 /usr/local/apps/amber12/bin/cpptraj
00836000-0084a000 rw-p 00000000 00:00 0
02087000-02819000 rw-p 00000000 00:00 0 [heap]
7f35bc000000-7f35bc021000 rw-p 00000000 00:00 0
7f35bc021000-7f35c0000000 ---p 00000000 00:00 0
7f35c09cd000-7f35c0c7e000 rw-p 00000000 00:00 0
7f35c0ff7000-7f35c102c000 r-xp 00000000 08:02 3031606 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f35c102c000-7f35c122b000 ---p 00035000 08:02 3031606 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f35c122b000-7f35c122c000 r--p 00034000 08:02 3031606 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f35c122c000-7f35c122d000 rw-p 00035000 08:02 3031606 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f35c122d000-7f35c13c6000 r-xp 00000000 08:02 2498587 /lib/x86_64-linux-gnu/libc-2.13.so
7f35c13c6000-7f35c15c5000 ---p 00199000 08:02 2498587 /lib/x86_64-linux-gnu/libc-2.13.so
7f35c15c5000-7f35c15c9000 r--p 00198000 08:02 2498587 /lib/x86_64-linux-gnu/libc-2.13.so
7f35c15c9000-7f35c15ca000 rw-p 0019c000 08:02 2498587 /lib/x86_64-linux-gnu/libc-2.13.so
7f35c15ca000-7f35c15d0000 rw-p 00000000 00:00 0
7f35c15d0000-7f35c15e5000 r-xp 00000000 08:02 2499200 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f35c15e5000-7f35c17e4000 ---p 00015000 08:02 2499200 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f35c17e4000-7f35c17e5000 r--p 00014000 08:02 2499200 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f35c17e5000-7f35c17e6000 rw-p 00015000 08:02 2499200 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f35c17e6000-7f35c1869000 r-xp 00000000 08:02 2498581 /lib/x86_64-linux-gnu/libm-2.13.so
7f35c1869000-7f35c1a68000 ---p 00083000 08:02 2498581 /lib/x86_64-linux-gnu/libm-2.13.so
7f35c1a68000-7f35c1a69000 r--p 00082000 08:02 2498581 /lib/x86_64-linux-gnu/libm-2.13.so
7f35c1a69000-7f35c1a6a000 rw-p 00083000 08:02 2498581 /lib/x86_64-linux-gnu/libm-2.13.so
7f35c1a6a000-7f35c1b52000 r-xp 00000000 08:02 3031635 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f35c1b52000-7f35c1d52000 ---p 000e8000 08:02 3031635 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f35c1d52000-7f35c1d5a000 r--p 000e8000 08:02 3031635 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f35c1d5a000-7f35c1d5c000 rw-p 000f0000 08:02 3031635 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7f35c1d5c000-7f35c1d71000 rw-p 00000000 00:00 0
7f35c1d71000-7f35c1e85000 r-xp 00000000 08:02 3031488 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f35c1e85000-7f35c2084000 ---p 00114000 08:02 3031488 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f35c2084000-7f35c2085000 r--p 00113000 08:02 3031488 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f35c2085000-7f35c2087000 rw-p 00114000 08:02 3031488 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f35c2087000-7f35c2096000 r-xp 00000000 08:02 2490395 /lib/libbz2.so.1.0.4
7f35c2096000-7f35c2295000 ---p 0000f000 08:02 2490395 /lib/libbz2.so.1.0.4
7f35c2295000-7f35c2296000 r--p 0000e000 08:02 2490395 /lib/libbz2.so.1.0.4
7f35c2296000-7f35c2297000 rw-p 0000f000 08:02 2490395 /lib/libbz2.so.1.0.4
7f35c2297000-7f35c22ae000 r-xp 00000000 08:02 2499262 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f35c22ae000-7f35c24ad000 ---p 00017000 08:02 2499262 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f35c24ad000-7f35c24ae000 r--p 00016000 08:02 2499262 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f35c24ae000-7f35c24af000 rw-p 00017000 08:02 2499262 /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7f35c24af000-7f35c24d0000 r-xp 00000000 08:02 2498585 /lib/x86_64-linux-gnu/ld-2.13.so
7f35c269d000-7f35c26a4000 rw-p 00000000 00:00 0
7f35c26ca000-7f35c26cf000 rw-p 00000000 00:00 0
7f35c26cf000-7f35c26d0000 r--p 00020000 08:02 2498585 /lib/x86_64-linux-gnu/ld-2.13.so
7f35c26d0000-7f35c26d2000 rw-p 00021000 08:02 2498585 /lib/x86_64-linux-gnu/ld-2.13.so
7fffc8a8e000-7fffc8aaf000 rw-p 00000000 00:00 0 [stack]
7fffc8b98000-7fffc8b99000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
vijay.glycosim:~/Simulation-Folder-Feb2013/chapter5-thermo-paper2-Vj/thermo2-Analysis/analysis-malto-/33_head_ring1_rotational_diff-malto-thermo$
I have also have posted message related to this issue under "rotational diffusion via cpptraj".
But seems I need some more clarification relating to this error and proper way of use to command according my need.
Advance many thanks
Vijay Manickam Achari
(Phd Student)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 05 2014 - 02:00:02 PST
