Hi
Is there any way that I can get the velocity values for specific step?
As after equlibrating the system is getting far away, at that lowest energy step is the structure I want.
________________________________
From: Thakur, Abhishek <axt651.miami.edu>
Sent: Thursday, January 26, 2017 12:54:20 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make restrt file for specific step
Yes, I have been saving velocities
As I was using , ntx=5, irest=1,
But I don't think I have velocity saved in any separate file.
As in my script I just produce restrt, crd and out file.
________________________________
From: Bill Ross <ross.cgl.ucsf.edu>
Sent: Thursday, January 26, 2017 12:34:33 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to make restrt file for specific step
Had you been saving velocities to mdvel, you could have extracted the
corresponding set of velocities and used it to create a restrt you could
run from.
Bill
On 1/26/17 1:13 PM, Bill Ross wrote:
> You will need to re-equilibrate to generate velocities.
>
> Bill
>
>
> On 1/26/17 12:57 PM, Thakur, Abhishek wrote:
>> Hi
>>
>> It worked with .rst7 extension.
>>
>>
>> But when I am putting that restrt file for aMD it is complaining could not find much information about velocity in the restrt
>>
>>
>>
>> ________________________________
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Sent: Thursday, January 26, 2017 9:30:16 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] How to make restrt file for specific step
>>
>> On Thu, Jan 26, 2017 at 3:08 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>>> trajin WT_avg_160ns.crd.gz 739 739
>>> trajout WT_avg_160ns_739.rst
>> Note that cpptraj does not recognize '.rst' as an Amber restart
>> extension - you are likely writing WT_avg_160ns_739.rst as an Amber
>> ASCII trajectory (to know for certain check the output from cpptraj -
>> it will tell you what format it is using for the output trajectory).
>>
>> Either use the extension '.rst7' or add the 'restart' keyword to your
>> 'trajout' line.
>>
>> -Dan
>>
>>> ./cpptraj -p WT.prmtop <ex.trajin> ex.out
>>>
>>> it forms restrt file but gives me an error when I try to make pdb file from rst file and check istructure.
>>> Ambpdb complains that atoms number does not match with prmtop file
>>>
>>>
>>> ________________________________
>>> From: Hai Nguyen <nhai.qn.gmail.com>
>>> Sent: Thursday, January 26, 2017 8:56:29 AM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] How to make restrt file for specific step
>>>
>>> Please see trajout command in cpptraj.
>>>
>>> (probably you just need
>>>
>>> parm your.parm7
>>> trajin your.nc 5000 5000 # just an example of your desired frame
>>> trajout your.rst7
>>> )
>>>
>>> Hai
>>>
>>> On Thu, Jan 26, 2017 at 2:52 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
>>>
>>>> Hi everyone,
>>>>
>>>>
>>>> I am doing aMD so after 10ns of production run I have extracted the lowest
>>>> energy structure at around 50steps.
>>>>
>>>> Can any one help me out, how to create restrt file for that particular
>>>> step of MD.
>>>>
>>>>
>>>>
>>>>
>>>> Thanking you,
>>>>
>>>> Abhishek
>>>> _______________________________________________
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>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.lobos.nih.gov_lcb&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=a6auFNIIlYHTuNiYRR-DXyBBrwH-hqDW_xQCi_ldegU&s=M9MSzUUL6VOGgQ9v4UDx_ROU_2IjtALtASGZ5kxRppk&e=
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Received on Fri Jan 27 2017 - 07:00:03 PST
