# Re: restarting umbrella sampling simulation.

From: ipsita basu (ibasu788_at_gmail.com)
Date: Mon Sep 10 2012 - 01:48:44 CDT

Thank you sir for your help as I've learnt a lot from you.
In the harmonic part regarding center, targetcenter etc I was wrong,
you are absolutely correct that I've to set center at 70 and target at
20. It is very much clear from the output.
Now when I did some analysis from the output dcd file, I found that
all the segments are moving equally from +z to -z direction. But I
only one segment to move which I had set in the group1 portion. This
part in the configuration file is like:
colvar {
width 1.0
name distanceZ
distance {
group1 {
atomNumbersRange 94313 - 97288
}
group2 {
dummyAtom ( 00.99, 00.39, -61.89 )
}
}
}
where group1 is defined above. I want the segment in group1 is moving
towards group2 keeping group2 fixed and as there is a large no in
group2 segment, I defined it like above.
And my desire is to decrease the distance between the two above
defined groups from the value set at centers to targetcenters only by
moving group1 without affecting the rest of the system.
But as the whole system is moving, the desired distance is not
decreasing,it initially decreases then increases. My questions are:
1.Is the selection mentioned above correct?
2.Should I put some position restraints to the system except group1?
3.Is there anything else I missed or I misunderstood?

On 9/5/12, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> On 5 September 2012 09:34, ipsita basu <ibasu788_at_gmail.com> wrote:
>> Sorry to bother you again. But I have again some doubts which I want
>> to make clear.
>> One point is:
>> If I set centers at 70.0, the traj file shows that the distance is
>> increasing from 68.3 and if I set centers at 60.0 then the distance is
>> decreasing from 68.3, from this observation I think that the initial
>> distance is 68.3 and it tries to reach to the value set at centers.
>
> Yes, this sounds right. Remember that the current value of the
> restraint centers are always in the NAMD output.
>
>> Then what is the importance of targetcenters,
>> targetnumsteps,targetnumstages etc.?
>
> If everything is set up right, they should matter.
>
>> Second point is:
>> From namd list I get an instruction “give a fixed center for the
>> harmonic restraint, and run the simulation for some time, then you
>> give a different center and repeat.” and according to your suggestion
>> not to change the configuration file when restarting the job.
>
> That is only if you want all your windows to be run sequentially, each
> one starting from the end of the previous one.
>
>> So can I
>> run the whole umbrella sampling simulation for just one time setting
>> centers at 20.0 (my desire is to change the distance from 68.3 to 20)
>> ?
>
> My guess is, you should keep centers at 70 and set targetCenters at 20.
>
>> Can't I analyze it with wham with only one traj file?
>
> Everything is possible.
>
>> And if the
>> above things are possible then what will be the value of targetcenters
>> in my configuration file when centers at 20.0?
>
> I don't think the value of centers should be 20 here.
>
> Jerome
>
>
>
>> On 9/4/12, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>>> Ipsita,
>>> Please keep the list in CC so that others can follow this conversation.
>>>
>>> The config file should not be changed for restarting (i.e. "centers
>>> 70" should stay that way), as NAMD should get from the restart file
>>> information about the current stage of the transformation.
>>>
>>> The very first stage should be numbered zero. Please look for output
>>> lines mentioning changes in restraint centers in the log file of the
>>> first NAMD run.
>>>
>>> Finally, be aware that targetNumSteps gives the number of steps per
>>> stage, not the total. The total simulation time should be
>>> (targetNumStages + 1) * targetNumSteps.
>>> The +1 is for sampling the last point: for 100 stages, there are 101
>>> points to be sampled.
>>>
>>> to improve it as we realize what's needed, thanks to user feedback
>>> like yours.
>>>
>>> Jerome
>>>
>>>
>>> On 4 September 2012 10:10, ipsita basu <ibasu788_at_gmail.com> wrote:
>>>> Whatever I choose the value of centers, keeping fixed targetCenters
>>>> 50.00 , the NAMD output is :
>>>> colvars: Moving restraint stage 1 : setting centers to { 59.802 }.
>>>> Then the center will move to 59.802 in the next 1000000 steps? Then
>>>> what is the meaning of setting centers, and targetCenters?
>>>> Yes I include the colvarsInput parameter as :
>>>> colvarsInput out-us/da-us-1.out.res.colvars.state
>>>>
>>>> On 9/4/12, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>>>>> Ipsita,
>>>>>
>>>>> Better than looking at the colvars trajectory, you can look in the
>>>>> NAMD output for lines saying :
>>>>> Moving restraint stage n : setting centers to x
>>>>>
>>>>> When restarting the job, do you add the colvarsInput parameter in the
>>>>> NAMD config file?
>>>>>
>>>>> Cheers,
>>>>> Jerome
>>>>>
>>>>>
>>>>>
>>>>> On 4 September 2012 07:42, ipsita basu <ibasu788_at_gmail.com> wrote:
>>>>>> Sir,
>>>>>> I have a query regarding restarting umbrella sampling simulation of
>>>>>> membrane protein system.
>>>>>> When I start it one portion of my configuration is:
>>>>>> harmonic {
>>>>>> name lenpot
>>>>>> colvars distanceZ
>>>>>> centers 70.00
>>>>>> forceConstant 5.0
>>>>>> targetCenters 60.00
>>>>>> targetNumSteps 1000000
>>>>>> targetNumStages 100
>>>>>> where the distance between the two selected group is 70 which I want
>>>>>> to decrease to 60 in 1000000 steps. The output traj is like:
>>>>>> 999800 6.04585123909563e+01
>>>>>> # step distanceZ
>>>>>> 1000000 6.04704550193212e+01
>>>>>> Now when I restart the job I set the above portion as :
>>>>>> harmonic {
>>>>>> name lenpot
>>>>>> colvars distanceZ
>>>>>> centers 60.00
>>>>>> forceConstant 5.0
>>>>>> targetCenters 50.00
>>>>>> targetNumSteps 1000000
>>>>>> targetNumStages 100
>>>>>> But doing this the output traj file is like:
>>>>>> 1403600 6.03582445087823e+01
>>>>>> 1403800 6.03622946744465e+01
>>>>>> which means the distance is not decreasing anymore, so I omit the
>>>>>> option centers 60.00 and then I get the error: Error: must define the
>>>>>> initial centers of the restraints.
>>>>>> So should I set the value for centers and target centers, then what
>>>>>> is
>>>>>> the difference between the two?
>>>>>> Or should I set off the options:
>>>>>> targetCenters 50.00
>>>>>> targetNumSteps 1000000
>>>>>> targetNumStages 100
>>>>>> --
>>>>>> Ipsita Basu
>>>>>> Research Fellow
>>>>>> c/o : Dr. Chaitali Mukhopadhyay
>>>>>> Rajabazar Science College
>>>>>> Kolkata - 700009
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Ipsita Basu
>>>> Research Fellow
>>>> c/o : Dr. Chaitali Mukhopadhyay
>>>> Rajabazar Science College
>>>> Kolkata - 700009
>>>
>>
>>
>> --
>> Ipsita Basu
>> Research Fellow
>> c/o : Dr. Chaitali Mukhopadhyay
>> Rajabazar Science College
>> Kolkata - 700009
>>
>

```--
Ipsita Basu
Research Fellow