VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Apr 27 2018 - 12:31:57 CDT

Like I said -- no such thing as "correct".
But if they agree with what you expect - that is good enough.

On Sat, Apr 28, 2018 at 5:25 AM, Sadegh Faramarzi Ganjabad <
safaramarziganjabad_at_mix.wvu.edu> wrote:

> Ashar,
>
> Yes I get the results and compare them with individual RMSD values I get
> from the RMSD plugin. The values are correct.
>
> Thanks,
> Sadegh Faramarzi,
> Research Assistant
> West Virginia University, Department of Chemistry
> Email:safaramarziganjabad_at_mix.wvu.edu
>
> On Fri, Apr 27, 2018 at 1:23 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> Please note that calculation of RMSD is a sub-optimal process. You can
>> never truly know if the solution is good enough.
>> Since this is just a warning and not an error, I am guessing you do get a
>> result? which I think you should. Is that result reasonable? If it is you
>> can ignore the warning.
>>
>> On Sat, Apr 28, 2018 at 4:38 AM, Sadegh Faramarzi Ganjabad <
>> safaramarziganjabad_at_mix.wvu.edu> wrote:
>>
>>> Hello,
>>>
>>> Thank you all for your comments. I have 385 lipids, but the error
>>> happened even for smaller number of residues. It seems deleting selections
>>> solves the problem. Now it does not take too much of memory, although it
>>> gives that error
>>>
>>> Matrix: Warning: no convergence (0.00000000<2177.16064453 after 1000
>>> iterations).
>>>
>>> Best,
>>> Sadegh Faramarzi,
>>> Research Assistant
>>> West Virginia University, Department of Chemistry
>>> Email:safaramarziganjabad_at_mix.wvu.edu
>>>
>>> On Fri, Apr 27, 2018 at 10:21 AM, Udaya Dahal <dahal.udaya_at_gmail.com>
>>> wrote:
>>>
>>>> If you want to delete all atom selection after each run, just use
>>>> foreach sel [atomselect list] {$sel delete}
>>>>
>>>> otherwise you have to explicitly delete variables as Brian mentioned.
>>>>
>>>> Regards,
>>>>
>>>> On Fri, Apr 27, 2018 at 9:59 AM, Brian Radak <brian.radak_at_gmail.com>
>>>> wrote:
>>>>
>>>>> +1 to Giacomo.
>>>>>
>>>>> For the record (although you should really read the documentation!)
>>>>> the syntax for deleting a selection freeing up memory is:
>>>>>
>>>>> <selection value> delete
>>>>>
>>>>> as in this pseudocode:
>>>>>
>>>>> set compare [atomselect top "residue 1"]
>>>>> for # iterate frames {
>>>>> $compare frame $frame
>>>>> <measure>
>>>>> }
>>>>> $compare delete
>>>>>
>>>>> I would hazard a guess that VMD attempts to clean up all such objects
>>>>> whenever it exits, but it will almost always be much better to delete them
>>>>> explicitly.
>>>>>
>>>>> On Fri, Apr 27, 2018 at 8:01 AM, Giacomo Fiorin <
>>>>> giacomo.fiorin_at_gmail.com> wrote:
>>>>>
>>>>>> Any atom selection created in VMD will take up memory. I'm not sure
>>>>>> if that's the cause in your case (how many POPC molecules are there?), but
>>>>>> you should remove the selections that you don't use any more. The
>>>>>> documentation of the atomselect command contains the syntax for that.
>>>>>>
>>>>>> Also, the "get" method for an atomselection returns the requested
>>>>>> property for each atom in the selection. Try printing the result of "get
>>>>>> residue".
>>>>>>
>>>>>> Giacomo
>>>>>>
>>>>>> On Fri, Apr 27, 2018 at 12:30 AM, Sadegh Faramarzi Ganjabad <
>>>>>> safaramarziganjabad_at_mix.wvu.edu> wrote:
>>>>>>
>>>>>>> Hello all,
>>>>>>>
>>>>>>> I am trying to calculate RMSD of individual lipids in a
>>>>>>> protein-lipid system. I found this code that aligns a single residue and
>>>>>>> gets the RMSD of the entire trajectory.
>>>>>>>
>>>>>>> # Prints the RMSD of the protein atoms between each timestep
>>>>>>> # and the first timestep for the given molecule id (default: top)
>>>>>>> proc print_rmsd_through_time {{mol top}} {
>>>>>>> # use frame 0 for the reference
>>>>>>> set reference [atomselect $mol "residue X" frame 0]
>>>>>>> # the frame being compared
>>>>>>> set compare [atomselect $mol "residue X"]
>>>>>>>
>>>>>>> set num_steps [molinfo $mol get numframes]
>>>>>>> for {set frame 0} {$frame < $num_steps} {incr frame} {
>>>>>>> # get the correct frame
>>>>>>> $compare frame $frame
>>>>>>>
>>>>>>> # compute the transformation
>>>>>>> set trans_mat [measure fit $compare $reference]
>>>>>>> # do the alignment
>>>>>>> $compare move $trans_mat
>>>>>>> # compute the RMSD
>>>>>>> set rmsd [measure rmsd $compare $reference]
>>>>>>> # print the RMSD
>>>>>>> puts "RMSD of $frame is $rmsd"
>>>>>>> }
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>> but when I iterate this code for all lipid residues it takes a lot of memory and my computer freezes. I'm not sure why. Here is the code I'm using
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> set selmode [[atomselect top "resname POPC"] get residue]
>>>>>>> #gets stdin selmode
>>>>>>> foreach r $selmode {
>>>>>>>
>>>>>>> # selection
>>>>>>> set reference [atomselect top "residue $r" frame 0]
>>>>>>> set compare [atomselect top "residue $r"]
>>>>>>> set num_steps [molinfo top get numframes]
>>>>>>> set output [open "rmsd_$r.dat" w]
>>>>>>> # rmsd calculation loop
>>>>>>> for {set frame 0} {$frame < $num_steps} {incr frame} {
>>>>>>> # get the correct frame
>>>>>>> $compare frame $frame
>>>>>>>
>>>>>>> # compute the transformation
>>>>>>> set trans_mat [measure fit $compare $reference]
>>>>>>> # do the alignment
>>>>>>> $compare move $trans_mat
>>>>>>> # compute the RMSD
>>>>>>> set rmsd [measure rmsd $compare $reference]
>>>>>>> # print the RMSD
>>>>>>> #puts "$r"
>>>>>>> puts $output "$rmsd"
>>>>>>> }
>>>>>>>
>>>>>>> close $output
>>>>>>>
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Does anybody know a better way of doing this?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Sadegh Faramarzi,
>>>>>>>
>>>>>>> Research Assistant
>>>>>>> West Virginia University, Department of Chemistry
>>>>>>> Email:safaramarziganjabad_at_mix.wvu.edu
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Giacomo Fiorin
>>>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>>>> Contractor, National Institutes of Health, Bethesda, MD
>>>>>> http://goo.gl/Q3TBQU
>>>>>> https://github.com/giacomofiorin
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>> --
>> Best,
>> /A
>>
>
> 

-- 
Best,
/A