Dear All
I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.
Original messge:
I am trying to prepare a solvation box of chaps. After generating .itp
and .gro at ProDrg and thorough check of charges, I started with a box
size of 6x6x6. Energy m
shahid nayeem wrote:
Dear All
I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.
Original messge:
I am trying to prepare a solvation box of chaps. After generating .itp
and .gro at ProDrg and thorough check of charges, I started with a bo
Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning
On 28/01/2011 3:51 PM, shahid nayeem wrote:
Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with cons
Please tell me where I am wrong. I downloaded pdb of chaps and used
prodrg server to get .itp and .gro file. Then I checked .itp for any
missing charge and I found it correct. Then I created 6.0x6.0x6.0 box
with genbox inserting 7 molecules of chaps.gro. Then again using
genbox and -maxsol I put 51
shahid nayeem wrote:
Please tell me where I am wrong. I downloaded pdb of chaps and used
prodrg server to get .itp and .gro file. Then I checked .itp for any
missing charge and I found it correct. Then I created 6.0x6.0x6.0 box
PRODRG doesn't have a problem of missing charges. It provides no
Hi Justin
Thanks a lot.
I tried doing energy minimization and th lowering emtotal to 200 and
the system converged to
Steepest Descents converged to Fmax < 200 in 1411 steps
Potential Energy = -3.9063050e+05
Maximum force = 1.3442458e+02 on atom 927
Norm of force = 1.4758101e+01
For equi
shahid nayeem wrote:
Hi Justin
Thanks a lot.
I tried doing energy minimization and th lowering emtotal to 200 and
the system converged to
Steepest Descents converged to Fmax < 200 in 1411 steps
Potential Energy = -3.9063050e+05
Maximum force = 1.3442458e+02 on atom 927
Norm of force =
shahid nayeem wrote:
I ran normal MD and it runs fine. Today I used six 10ps MD keeping
temperature 300 K and each time gradually increasing pressure from 1
bar to 5 bar to 25, 50, 75 and then 100bar. It all ran successfully.
Thereafter doing simulated annealing for cooling and heating and
equi
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