[gmx-users] Incorrect dihedral restraints

[Jonathan Khao]

Hi, 

I'm using the 3.3.1 version, so the 3.2 bugs should have been fixed. 
The constraints that I have applyed are weak because the dihedrals of
the helix that I want to "straighten" are far from the theorical 57°
( some are around 85° ). Since it is a harmonic potential, and that i
want a "soft" straightening, i thought that it would be OK .

I have aleready tryed to put stronger restraints  :
	dihre                    = Simple
	dihre-fc                 = 1000
	dihre-tau                = 1
	nstdihreout              = 100	
but the following errors occur :

==================================================================
[ Numerous LINCS warnings ]

Warning: 1-4 interaction between 90 and 98 at distance 1.818 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

Step 52, time 0.104 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     75     76   90.0    0.1142   0.1815      0.1000
     80     81   47.7    0.0994   0.1003      0.1000
     80     82   38.0    0.1475   0.1822      0.1470
     82     83   44.8    0.1538   0.2199      0.1530
     82     86  123.3    0.1533 236577931264.0000      0.1530
     86     87  152.9    0.1232 236577931264.0000      0.1230
     86     88  110.6    0.1326 1367999643648.0000      0.1330
     88     89  102.8    0.1434 1333306720256.0000      0.1000
     88     90   93.5    0.1460 12990258610176.0000      0.1470
     90     91   95.1    0.1536 12554454695936.0000      0.1530
     90     95   87.7    0.1776 112384387579904.0000      0.1530
  [etc ... ]


Step 53  Warning: pressure scaling more than 1%, mu: 1.00971e+27
1.00971e+27 1.00971e+27
[ other pressure scaling warnings ]

-------------------------------------------------------
Program mdrun_mpi, VERSION 3.3
Source code file: nsgrid.c, line: 220

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

-------------------------------------------------------

"Torture You.... Yeah, That's a Good Idea, I Like That." (Pulp Fiction)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 4

gcq#27: "Torture You.... Yeah, That's a Good Idea, I Like That." (Pulp
Fiction)

-----------------------------------------------------------------------------
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 21713 failed on node n0 (10.234.64.179) with exit status 1.
-----------------------------------------------------------------------------

=========================================================================

So i assume that i get warnings because of the important changes that
occur due to the dihedral restraints applyed, especially for 
" max 32832334180909056.000000 (between atoms 97 and 98) rms
1106664761589760.000000 " and for the 1-4 warning  :) 
Which is probably the cause of the crash ...

Now for the 1-4 distance warning , it seems that the restraints applyed
tear apart some 1-4 bonds ... So have a doubt conerning the order of
atoms in the dihedral index file. 
Correct me if i'm wrong, i want to mesure phi angles , so my index file
contain these atoms in the following order :   C  N   Ca   C ?


Thank you for your help, I have been working on this problem for few
days now , and it gets verry frustrating ...

KHAO Jonathan 


>What version of GROMACS are you using? Also, your force constants seem
>sort of small. Have you tried larger values?
>
>David


>On 3/20/07, Jonathan Khao <jkhao at ibsm.cnrs-mrs.fr> wrote:
>> Hello
>>
>>         My goal is to make dihedral restraints on the backbone of a bent
>>         alpha
>>         helix to obtain its original structure. I've looked through the
>>         mailing
>>       list, followed the instructions, applyed some dihedrals around
>>         57° but
>>         the obtained dihedrals are all close to 180°.
>>
>>         in my Top file, i have included the following lines
>>         [ dihedral_restraints ]
>>         ; A  B  C   D    type   label   angle  delta   kfac    pow
>>          56 58  60  73     1      6     -63.5   0       1       2
>>          73 75  77  78     1      7     -57.6   0       1       2
>>
>>         and in the mdp file :
>>         dihre                    = Simple
>>         dihre-fc                 = 100
>>         dihre-tau                = 0
>>         nstdihreout              = 100
>>
>>         What am i doing wrong ?
>>
>>         Thanks !
>>         Jonathan Khao
>>
>>
>>
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