[gmx-users] gromacs Query
Justin Lemkul
jalemkul at vt.edu
Fri Apr 7 14:05:10 CEST 2017
On 4/7/17 6:17 AM, Aman Deep wrote:
> sir, I didn't understand what is E here ???
>
I think Mark made a typo in writing the word "maybe" here.
The point he was making is that you're trying to specify nstxtcout and
nstxout-compressed, which is a mixture of syntax from different GROMACS
versions. You can't/shouldn't do that.
> and after removing nstxout still, it is not helping..
>
All of the .trr options (nstxout, nstvout, nstfout) default to zero, so a .trr
file is only written if you ask for it by setting any one of those to a non-zero
value.
-Justin
> On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Which version of GROMACS is this? The only problem I can see is that you
>> are using both nstxtcout and its successor (don't), and may E that is
>> confusing the parser.
>>
>> Mark
>>
>> On Fri, 7 Apr 2017 07:41 Aman Deep <r.amandeep2677 at gmail.com> wrote:
>>
>>> sir, i am using this output control but still, it is generating same
>> space
>>> data
>>>
>>>
>>> ; Run parameters
>>> integrator = md ; leap-frog integrator
>>> nsteps = 25000000 ; 2 * 500000 = 50000 ps (50 ns)
>>> dt = 0.002 ; 2 fs
>>>
>>> ; Output control
>>> nstxout = 0 ; save coordinates every 10.0 ps
>>> nstxtcout =2500000 ; save velocities every
>>> 50.0 ps
>>> nstenergy = 2500000 ; save energies every
>> 50.0
>>> ps
>>> nstlog = 2500000 ; update log file every 50.0 ps
>>> nstxout-compressed = 2500000 ; save compressed coordinates every
>> 10.0
>>> ps ; nstxout-compressed replaces nstxtcout
>>> xtc-grps = Protein ; replaces xtc-grps
>>>
>>>
>>> On Mon, Apr 3, 2017 at 3:15 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> If you ask for .trr output, you get it. Stop using non-zero nst*out mdp
>>>> settings that you don't want.
>>>>
>>>> Mark
>>>>
>>>> On Mon, Apr 3, 2017 at 11:31 AM Aman Deep <r.amandeep2677 at gmail.com>
>>>> wrote:
>>>>
>>>>> sir,
>>>>>
>>>>> I have tried *nstxctout *but it still making trr file ... is there
>> any
>>>>> option to make only xtc file ???
>>>>>
>>>>> On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham <
>> mark.j.abraham at gmail.com
>>>>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> See
>>>>>>
>>>>> http://www.gromacs.org/Documentation/How-tos/
>>>> Reducing_Trajectory_Storage_
>>>>>> Volume
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> On Mon, Apr 3, 2017 at 9:27 AM Aman Deep <r.amandeep2677 at gmail.com
>>>
>>>>> wrote:
>>>>>>
>>>>>>> sir is there any way to create only XTC file from mdrun only. the
>>>>> server
>>>>>> on
>>>>>>> which I am working is not providing enough space and my trr file
>> is
>>>> too
>>>>>>> much large.
>>>>>>>
>>>>>>> thank you
>>>>>>>
>>>>>>> --
>>>>>>> Aman Deep
>>>>>>> MSc Bioinformatics
>>>>>>> Jamia Millia Islamia
>>>>>>> New Delhi - 110025
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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>>>>>
>>>>>
>>>>> --
>>>>> Aman Deep
>>>>> MSc Bioinformatics
>>>>> Jamia Millia Islamia
>>>>> New Delhi - 110025
>>>>> --
>>>>> Gromacs Users mailing list
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>>>
>>>
>>>
>>> --
>>> Aman Deep
>>> MSc Bioinformatics
>>> Jamia Millia Islamia
>>> New Delhi - 110025
>>> --
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>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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