[gmx-users] size of the molecule

[raj vel]

hello all,
i am unable to do mdrun, for a protein with 504
aminoacids. while mdrun, LINCS warning and the
pressure coupling is more than 1 amu and this aborts
the mdrun. i was informed to increase tau_p, even that
is not working. 
but when i split the molecule (from PDB) into 100
aminoacid each, mdrun runs properly. but the time
taken by each fragment for mdrun differs very high.(
45 min for one segment and 48 hours for another
segment).

is that possible to do mdrun for a molecule with such
high no. of amino acids??
any suggestions


FURTHER INFO:
i use protein in water.
there is no ligand and hetero atoms in the protein.
i used default for box size.
the error is:
...
Step -2, time -0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.113290 (between atoms 5739 and 5741) rms
0.002287
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint
length
   5739   5740   39.6    0.1032   0.1014      0.1000
   5741   5742   62.8    0.1104   0.1148      0.1090
   5741   5743   60.5    0.1083   0.1129      0.1090
   5741   5744   42.8    0.1435   0.1654      0.1530
starting mdrun 'Protein in water'
500000 steps,   1000.0 ps.


Back Off! I just backed up full.trr to ./#full.trr.22#

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 427.582703 (between atoms 5894 and 5895) rms
12.626502
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint
length
   5722   5724   35.1    0.1471   0.1793      0.1470
....

Warning: 1-4 interaction at distance larger than 1
These are ignored for the rest of the simulation
turn on -debug for more information

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 574.704163 (between atoms 5731 and 5732) rms
20.365654
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint
length
   5720   5721   34.9    0.1252   0.1391      0.123
.....
Back Off! I just backed up step0.pdb to
./#step0.pdb.22#

Step 1  Warning: pressure scaling more than 1%, mu:
1.01435 1.01435 1.01435

Step 1  Warning: pressure scaling more than 1%, mu:
1.01435 1.01435 1.01435

Back Off! I just backed up step1.pdb to
./#step1.pdb.22#
Wrote pdb files with previous and current coordinates

Step 1  Warning: pressure scaling more than 1%, mu:
1.01435 1.01435 1.01435
Warning: Only triclinic boxes with the first vector
parallel to the x-axis and the second vector in the
xy-plane are supported.
         Box (3x3):
 Warning: Only triclinic boxes with the first vector
parallel to the x-axis and the second vector in the
xy-plane are supported.
         Box (3x3):
            Box[    0]={          nan,          nan,  
       nan}
......

Fatal error: ci = -1 should be in 0 .. -1 [FILE
nsgrid.c, LINE 210]
Error on node 0, will try to stop all the nodes
Fatal error: ci = -1 should be in 0 .. -1 [FILE
nsgrid.c, LINE 210]
Error on node 1, will try to stop all the nodes
Fatal error: ci = -1 should be in 0 .. -1 [FILE
nsgrid.c, LINE 210]
Error on node 2, will try to stop all the nodes
-----------------------------------------------------------------------------

One of the processes started by mpirun has exited with
a nonzero exit
code.  This typically indicates that the process
finished in error.
If your process did not finish in error, be sure to
include a "return
0" or "exit(0)" in your C code before exiting the
application.

PID 26459 failed on node n0 with exit status 1.
-----------------------------------------------------------------------------


THANKS IN ADVANCE..


=====
ALAGURAJ.V
STRUCTURAL BIOLOGY LAB,
MADURAI KAMARAJ UNIVERSITY.

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