Fwd: [gmx-users] Generation of the Distance Restraints

James Starlight jmsstarlight at gmail.com
Wed Mar 14 16:38:52 CET 2012 

Mark,


My restrains on topology consist of the next section

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ dihedral_restraints ]
; ai   aj    ak    al  type  label  phi  dphi  kfac  power
; Chi N - CA - CB - CG
  2908    2910     2911    2912     1      1  180     0     1      2

[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
  1097 3201 1    1     1     0.796 0.841 0.900 1.0
  2948 3201 1    2     1     0.796 0.841 0.900 1.0
  1097 2948 1    3     1     0.796 0.841 0.900 1.0
  1097 2999 1    4     1     0.800 1.000 1.100 1.0
  1098 2034 1    5     1     0.800 1.000 1.100 1.0
  1098 2042 1    6     1     0.800 1.000 1.100 1.0
  1098 2067 1    7     1     0.800 1.000 1.100 1.0
  1130 3241 1    8     1     0.540 0.630 0.700 1.0
  546  3393 1    9     1     1.162 1.725 1.800 1.0
  628  3460 1    10     1     1.438 2.067 2.100 1.0
  637  3460 1    11     1     0.700 1.238 1.300 1.0
  648  2791 1    12     1     1.788 2.152 2.200 1.0
  648  3376 1    13     1     1.736 2.061 2.150 1.0
  2292 2743 1    14     1     0.200 0.300 0.350 1.0
  1258 2203 1    15     1     0.200 0.300 0.350 1.0

Also I've attached my md.mdp file.

I have no problems with that system on my home desktop.

On cluster with installed MPI I've lunch my simulation by means of below
command

grompp -f md.mdp -c nvtWprotonated.gro -p topol.top -n index.ndx -o
md_50ns.tpr

mpiexec -np 24 mdrun_mpi_d.openmpi -v -deffnm md_50ns


I'll be very thankful if you show me what's wrong could be with my initial
systems because I have no any problems with my systems on my home desktop.
On the other hand on Cluster some of my jobs ends with the errors (
something wrong with PME order or the error wich I've shown you with the
ensembles of restrains)

It was installed the same last version of Gromacs on cluster like on my
desctop ( difference only in double precission with lack on my home desctop
but present on cluster)

Could you tell me in what log files I could obtain more detailed
information of the source of such erors? I've checked only md.log as well
as name_of_the_simulation.log. Besides there are files gromacs.err wich
contain information about crashed simulation.



Thanks for help again,


James

14 марта 2012 г. 16:10 пользователь Mark Abraham
<Mark.Abraham at anu.edu.au>написал:

>  You're probably doing something wrong, but in the absence of a command
> line and your .top file fragment, we can't possibly know.
>
>
> Mark
>
>
>
> Thanks for help again,
>
>
> James
>
> 14 марта 2012 г. 10:50 пользователь James Starlight <
> jmsstarlight at gmail.com> написал:
>
>> Mark, thanks for explanation.
>>
>> So if I understood that graph correctly I must define R1=1 and R2=2
>> values from my example 1<Rij<2 to obtain quadratic restrain forces done in
>> my distance range ( from 1 to 2 angstr). In other words this would
>> restrains the i and j atom to the desired distance by the force wich would
>> increased by the quadratic progresion upon distance will increased up to 2.
>> Does it correct ?
>>
>> So the value R0 ( no forces= no restraints) must correspond to the values
>> above and below my range. How the same range value for R0 could be defined ?
>>
>>
>> JAmes
>>
>> 14 марта 2012 г. 3:42 пользователь Mark Abraham <Mark.Abraham at anu.edu.au>написал:
>>
>>
>>>
>>> I can't think of a clearer way to explain the functional form of the
>>> distance restraint than the given equation with an example graph of it
>>> nearby. You have some distance range that you want to see happen based on
>>> some external information. You need to choose the distance constants for
>>> that functional form to reproduce that in a way that you judge will work,
>>> given your initial distance. The linear regime above r_2 is useful for not
>>> having forces that are massively large (from a quadratic potential) far
>>> from the region of zero potential. Whether this is important depends on
>>> your starting configuration.
>>>
>>>
>>>
>>>>
>>>>  I already answered this.
>>>>> http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html
>>>>>
>>>> I've found only theoretical explanation of such possibility (
>>>> gradually increasing force constant during simulation). But I
>>>> intresting in practical implementation. Could I do it in scope of
>>>> single MDrun by some options in mdm fle or should I do step-by-step
>>>> series of simulation with gradually changing forces appplied on the
>>>> disres in each MDrun?
>>>>
>>>
>>>  Only step by step. Something like simulated annealing is only available
>>> for temperature variation.
>>>
>>> Mark
>>>
>>>>
>>>>
>>>> James
>>>>
>>>
>>> --
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>>
>>
>
>
>
>
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