Re: [gmx-users] solvation_box_preparation

2011-02-09 Thread Justin A. Lemkul
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 =

Re: [gmx-users] solvation_box_preparation

2011-02-09 Thread Justin A. Lemkul
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

Re: [gmx-users] solvation_box_preparation

2011-02-08 Thread shahid nayeem
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

Re: [gmx-users] solvation_box_preparation

2011-01-30 Thread shahid nayeem
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

Re: [gmx-users] solvation_box_preparation

2011-01-30 Thread Justin A. Lemkul
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

[gmx-users] solvation_box_preparation

2011-01-27 Thread shahid nayeem
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

Re: [gmx-users] solvation_box_preparation

2011-01-27 Thread Justin A. Lemkul
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

Re: [gmx-users] solvation_box_preparation

2011-01-27 Thread shahid nayeem
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

Re: [gmx-users] solvation_box_preparation

2011-01-27 Thread Mark Abraham
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