[gmx-users] help regarding peptide in DMPC

[Itamar Kass]

   Dear all, I will be happy to have someone help regarding a my system.  Its is
composed of a homogeneous  tetra-peptide in DMPC bilayer.  After embedded the
protein in the lipid I did energy minimization.  The next step was to do some
position restrained dynamics, but NPT simulation crashed after few hundred step,
hence I first did few 5ps of NVT run and then 20ps of NPT.
   Then I start the MD, the md.mpd was:
cpp                 =  /usr/bin/cpp
integrator          =  md
dt                  =  0.002	
nsteps              =  500000
nstcomm             =  1
nstxout             =  200
nstvout             =  0
nstfout             =  0
nstlist             =  10 
ns_type             =  grid
rlist               =  1.5
coulombtype		=  PME
rcoulomb            =  1.5
rvdw                =  1.5
fourierspacing		=  0.12
fourier_nx		=  0
fourier_ny		=  0
fourier_nz		=  0
pme_order		=  6
ewald_rtol		=  1e-5
optimize_fft		=  yes

; Berendsen temperature coupling is on in three groups
Tcoupl              =  berendsen
tau_t               =  0.1	0.1  0.1  0.1
tc-grps		    =  protein  sol  DMPC Na
ref_t               =  310	310  310  0.1

; Pressure coupling is on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0

; Generate velocites is on at 310 K.
gen_vel             =  yes
gen_temp            =  310

first the simulation looked good, but then I got this error:

Wrote pdb files with previous and current coordinates
step 144950, will finish at Mon Sep 29 02:57:13 2003
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]={         NaNWarning: Only triclinic boxes with the first
vector parallel to the x-axis and the second vector in the xy-plane are supported.
, 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):
         NaN          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]={,          Box[    0]={         NaN          NaN, ,  
       NaN          NaN         Box[    0]={,          NaN         NaN, }
,             Box[    1]={         NaN         NaN         NaN}
,          NaN         NaN,          NaN }
}
   ,            NaN         Box[    1]={          Box[    2]={ }
         NaN          NaN   ,          Box[    1]={         NaN         Box[   
1]={         NaNWarning: Only triclinic boxes with the first vector parallel to
the x-axis and the second vector in the xy-plane are supported.
, , ,          NaN         NaN         NaN, }
         Can not fix pbc.
         NaN, ,          Box (3x3):
         NaN          NaN         NaN ,           Box[    0]={         NaN     
   NaN}
}
,          NaN  ,   } etc.

   I did not realize if the problem is the box or the pressure coupling, or
maybe other thing.
   If someone can tell me what is wrong, give me a clue, tell me of a tool to
check the system, or maybe of a way to solve the problem I will be very happy.
                        Happy new Jewish year to all of you, Itamar.


********************************************
Computers are like airconditioners... They don't work well with Windows
open.
********************************************

===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
============================================

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