[gmx-users] pressure scaling more than 1%

[nanyu101]

Dear gmx-users,
  I have try to make a hole for my ion channel.
grompp -f run.mdp -o insert.tpr -c dppc.pdb -r dppc.pdb -p dppc.top
mdrun -v -hole -holep hp.mdp -deffnm insert
 
But the system told as follows.And I will show you my run.mdp later.

Step 631  Warning: pressure scaling more than 1%, mu: 1.04684 1.04684 1.04684

Step 632  Warning: pressure scaling more than 1%, mu: 104.213 104.213 104.213

Step 633  Warning: pressure scaling more than 1%, mu: 2.66535e+07 2.66535e+07 2.66535e+07
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}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
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}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
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}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
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}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
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}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
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}
            Box[    1]={         nan,          nan,          nan}
            Box[    2]={         nan,          nan,          nan}
         Can not fix pbc.
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]


Pressure Coupling:

title               =  Yo
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  none
integrator          =  md
dt                  =  0.001	; ps !
nsteps              =  5000	; total 10 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  0.8
rcoulomb            =  1.4
rvdw                =  0.8
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  DPP	SOL
tau_t               =  0.1	0.1
ref_t               =  300	300
; Energy monitoring
energygrps	    =  DPP	SOL
; Pressure coupling is not on
Pcoupl              =  berendsen
tau_p               =  2.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  no


Would anyone give me any suggestions?Thanks very much.

Best wishes,
Xianhui Wu
______________________________________

===================================================================
ÊÖ»úÓïÒôÁÄÌì¹úÄÚ³¤Í¾5·ÖÖÓ/1Ôª¡¢Ë§¸çÃÀÅ®ö¦ÕÕ¾¡ÔÚ°®Çé¿ìµÝ (http://love.sina.com.cn)
ÊÖ»ú¶ÌÐÅ·¢ËÍmµ½888810£¬Ãâ·Ñ»ñµÃÐÂÀË15MÈÎÄãÓÊÓÊÏ䣡 (http://vip.sina.com/love_send/lover.html)
çÍ·×ÏÂÔؾãÀÖ²¿ ÿÔÂ5ԪͼƬÁåÉùËæÐÄ»» (http://sms.sina.com.cn/act/member.html)