subject:"\[gmx\-users\] cannot open traj.xtc"

Re: [gmx-users] cannot open traj.xtc

2015-11-20 Thread 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  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

jalem...@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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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Re: [gmx-users] cannot open traj.xtc

2015-11-19 Thread surbhi mahajan

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.
Please suggest me where i am going wrong.
Thanks in advance.

Regards
Surbhi
On Wed, Nov 18, 2015 at 6:11 PM, Justin Lemkul  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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] cannot open traj.xtc

2015-11-18 Thread Justin Lemkul




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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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[gmx-users] cannot open traj.xtc

2015-11-17 Thread surbhi mahajan

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.
Thanks in advance.

Regards
Surbhi Mahajan
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] cannot open traj.xtc

Re: [gmx-users] cannot open traj.xtc

Re: [gmx-users] cannot open traj.xtc

[gmx-users] cannot open traj.xtc

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