Dear Amber users,
I am doing PMF calculation and i have problem with using restrain, I need to restrain system in Z direction and allow it to move only in xy direction, I have used distance restrain only at begning but my system was moving in z direction, then i applied an additional plane to point angle restrain using an angle 90 degree. I perform the minimization which goes normally, but when i perform equilibration (which include distance and point to plane restrain) only 8000 step is done out 250000 step using NVT or NPT and then stop. I did not see any error in the output file. I have checked for overlap using petraj and i did not see any, and i have checked the trajectories which did not show any strange behaviour.
I have attached the out file and error massage .
Could someone help me to solve this problem?
The restrain input file is as follows:
&rst
iat=1096,1097,1099,1100,-1,
igr1=531,556,561,560,535,534,
r1=-90., r2=90., r3=90., r4=270., rk2=1, rk3=1,
nstep1=1,nstep2=200000,
irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
r1a=-180., r2a=90., r3a=90., r4a=270., rk2a=0.010, rk3a=1.,
/
&rst
iat=-1, -1,
igr1=531,556,561,560,535,534,
igr2=1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,
r1=0.0, r2=3.0, r3=3.0, r4=99.,
rk2=2.39, rk3=2.39,
nstep1=1,nstep2=200000,
irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
r1a=0., r2a=3.0, r3a=3.0, r4a=99., rk2a=0.010, rk3a=2.39,
/
&rst
iat=1096,1097,1099,1100,-1,
igr1=531,556,561,560,535,534,
r1=-90., r2=90., r3=90., r4=270., rk2=1.0, rk3=1.0,
nstep1=200000,nstep2=250000,
irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
/
&rst
iat=-1, -1,
igr1=531,556,561,560,535,534,
igr2=1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,
r1=0.0, r2=3.0, r3=3.0, r4=99.,
rk2=2.39, rk3=2.39,
nstep1=200000,nstep2=250000,
irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
/
Regards
Rasha
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- application/octet-stream attachment: eq3.out
Received on Mon Mar 17 2014 - 05:30:03 PDT
