[gmx-users] No Distribution?

[Xu Dong Huang]

@ Gromacs users,

so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1    2    3, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following
There are no distances measured, that cannot be right. 

   0.0000000    0.0000000    0.0000000    0.0000000    0.0000000
  20.0000000    0.0000000    0.0000000    0.0000000    0.0000000
  40.0000000    0.0000000    0.0000000    0.0000000    0.0000000
  60.0000000    0.0000000    0.0000000    0.0000000    0.0000000
  80.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 100.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 120.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 140.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 160.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 180.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 200.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 220.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 240.0000000    0.0000000    0.0000000    0.0000000    0.0000000
 260.0000000    0.0000000    0.0000000    0.0000000    0.0000000
…

Thanks in advance,

Xu Huang


On Nov 2, 2013, at 6:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> On 11/2/13 6:29 PM, Xu Dong Huang wrote:
>> Dear All,
>> 
>> My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 1&2, 1&3 and 2&3, and I execute the following:
>> g_bond -f npt.xtc -n index.ndx -o bonds.xvg
>> 
>> I get the following error:
>> Total number of samples               : 153
>> Mean                                  : 0.501255
>> Standard deviation of the distribution: 0.152864
>> Standard deviation of the mean        : 0.0123583
>> 
>> Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1#
>> 
>> -------------------------------------------------------
>> Program g_bond, VERSION 4.5.5
>> Source code file: gmx_bond.c, line: 207
>> 
>> Fatal error:
>> No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> Upon inspecting my index files, I see that it defines my 3 particle group as:
>> [ O1 ]
>>    1    2    3
>> 
>> Then I changed the particle group index file to
>> [ O1 ]
>>    1    2
>>    2	3
>>    1	3
>> 
>> And I’m still getting the same error.
>> 
>> Any insights?
>> 
> 
> Use g_dist instead and measure the distances manually.  g_analyze can then produce a distribution of those data.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> 
> ==================================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists