[gmx-users] increase the time frame

[aiswarya pawar]

After running this minimization when i did gmxcheck i got this output

trn version: GMX_trn_file (single precision)
Reading frame       0 time    9.000
# Atoms  4113
Reading frame       3 time   57.000
Timesteps at t=31 don't match (12, 26)
Reading frame       4 time   69.000
Timesteps at t=57 don't match (26, 12)
Reading frame      14 time  192.000
Timesteps at t=184 don't match (13, 8)
Last frame         14 time  192.000


Item        #frames
Step            15
Time            15
Lambda          15
Coords          15
Velocities       0
Forces           0
Box             15


why is it saying that Timesteps at t=31 don't match (12, 26).


On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 21/10/2011 5:09 PM, aiswarya pawar wrote:
>
>> Hi users,
>>
>> Iam running a minimization on protein complex in vacuum. i have set the
>> parameters as following-
>>
>> ; Lines starting with ';' ARE COMMENTS
>> ; Everything following ';' is also comment
>>
>> title        = Energy Minimization    ; Title of run
>>
>> ; The following line tell the program the standard locations where to find
>> certain files
>> cpp        = /lib/cpp    ; Preprocessor
>>
>>
>> ; Define can be used to control processes
>> define          = -DFLEXIBLE
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator    = steepest        ; Algorithm (steep = steepest descent
>> minimization)
>> emtol        = 1000.0       ; Stop minimization when the maximum force <
>> 1.0 kJ/mol
>> emstep      = 0.01
>> nsteps        = 50000        ; Maximum number of (minimization) steps to
>> perform
>> nstenergy    = 1          ; Write energies to disk every nstenergy steps
>> energygrps    = Protein    ; Which energy group(s) to write to disk
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstxout     = 1
>> nstlist        = 10        ; Frequency to update the neighbor list and
>> long range forces
>> ns_type        = grid      ; Method to determine neighbor list (simple,
>> grid)
>> rlist        = 1.0        ; Cut-off for making neighbor list (short range
>> forces)
>> coulombtype    = cutoff       ; Treatment of long range electrostatic
>> interactions
>> rcoulomb    = 1.0        ; long range electrostatic cut-off
>> rvdw        = 1.4        ; long range Van der Waals cut-off
>> constraints    = none        ; Bond types to replace by constraints
>> pbc        = no            ; Periodic Boundary Conditions (yes/no)
>>
>> But from this i could write only 2 frames i need to increase the time
>> frames, what is to be changed in the parameters.
>>
>
> This will write every frame of the EM, but if it only has two steps...
>
> Mark
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