[gmx-users] cannot open traj.xtc

[Justin Lemkul]

On 11/20/15 2:10 AM, surbhi mahajan wrote:
> Thankyou sir,
> After using g_order -s md_0_1.tpr -f md_0_1.tpr.trr -n sn1.ndx -d z -od
> deuter_sn1.xvg
> the file order.xvg is created but still my file does not give any
> information about the system whether it is in gel phase or liquid phase.

The program calculates order parameters, it doesn't do your thinking for you. 
You have to interpret the contents of the deuter_sn*.xvg files and, in 
conjunction with other qualitative and quantitative data, make an assessment of 
what your bilayer is doing.

-Justin

> Please suggest me where i am going wrong.
> Thanks in advance.
>
> Regards
> Surbhi
> On Wed, Nov 18, 2015 at 6:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/18/15 2:45 AM, surbhi mahajan wrote:
>>
>>> Dear users,
>>> I am M.Sc student , I have been doing my simulations on lipids , I am
>>> stuck
>>> at the analysis part in which i want to calculate deuterium order
>>> parameter
>>> after I give the command:
>>> g_order -s md_0_1.tpr -n sn1.ndx -d z -od deuter_sn1.xvg
>>> I get the error cannot open file traj.xtc. please help me in solving this
>>> error.
>>>
>>
>> You didn't specify a trajectory file name (-f argument) so g_order looks
>> for the default name (traj.xtc) and it doesn't exit.  Specify a proper
>> input file name.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

==================================================