VMD-L Mailing List

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Fri Apr 27 2018 - 12:25:06 CDT

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
>