Re: [AMBER] Is there a way to compare trajectories?

From: Osman, Roman <roman.osman.mssm.edu>
Date: Thu, 11 Feb 2016 15:40:50 +0000

Karolyn's
My colleague Mihaly Mezei implemented a 2D rmsd comparison of two trajectories.
Please contact him. Mihaly.mezei.mssm.edu

I used it and it's a great tool

Roman Osman
Sent from my iPhone

> On Feb 11, 2016, at 4:45 AM, Karolina Markowska <markowska.kar.gmail.com> wrote:
>
> Thank you, Bill and Anselm for your advices,
>
> I think I will try the 2D-RMSD-plot first.
>
> Have a nice day!
> Karolina
>
> 2016-02-11 10:27 GMT+01:00 Dr. Anselm Horn <anselm.horn.fau.de>:
>
>> Dear Karolina,
>>
>> AFAIK a 'reference' is limited to a single structure.
>>
>> Reading in two trajectories in a row should be no problem for cpptraj,
>> as you can give several trajin commands.
>> For the comparison of the two trajectories you could then use e.g. a
>> 2D-RMSD-plot or perform a cluster analysis on the combined trajectories
>> with a subsequent inspection of the distribution of the cluster
>> structures between the trajectories. Or you could monitor some other
>> properties of interest and compare those values.
>>
>> Regards,
>>
>> Anselm
>>
>>
>> Am 11.02.2016 10:07, schrieb Karolina Markowska:
>>> Dear Amber Users,
>>>
>>> I have two simulations with the same system and I would like to compare
>>> them. Mostly I would like to check if I'm having the same protein
>>> conformations in these two simulations. Does Amber software provide a
>> tool
>>> for that kind of analysis?
>>>
>>> I wanted to use cpptraj and use the first trajectory as reference, add
>> the
>>> second one by trajin and calculate rmsd between them, but cpptraj uses
>> only
>>> the first frame from that file. Can I make cpptraj to read whole
>> trajectory
>>> as a reference?
>>> The script looked like that:
>>>
>>> parm protein.prmtop
>>> reference sim1.nc
>>> trajin sim2.nc
>>> autoimage
>>> strip :WAT
>>> strip :Na+
>>> rms ToRef :1-340.CA,C,N= reference out rmsd.arg mass
>>> quit
>>>
>>> | sim1.nc is the trajectory of the first simulation and sim2.nc is the
>>> trajectory from the second simulation.
>>>
>>> Thanks for your help.
>>> Best regards,
>>> Karolina Markowska
>>> PhD student
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e=
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e=
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=KGmK9QeuQGXU7AfWRng1JopBHi5t89pb6Jler12nUVM&s=5BH1TxzxAz0WEJlWLjovtEOPmgsq-547ySiRojtBe6U&e=

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 11 2016 - 08:00:05 PST
Custom Search