[gmx-users] rerun trajectory does not match input file
Justin A. Lemkul
jalemkul at vt.edu
Sat May 22 16:12:50 CEST 2010
John Shultz wrote:
> Why do I get this message saying the group is empty?
>
>
>
> Analysing residue names:
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> There are: 11350 OTHER residues
> There are: 244 PROTEIN residues
> There are: 0 DNA residues
> Analysing Protein...
> Analysing Other...
>
> 0 System : 37770 atoms
> 1 Protein : 3848 atoms
> 2 Protein-H : 1980 atoms
> 3 C-alpha : 244 atoms
> 4 Backbone : 732 atoms
> 5 MainChain : 974 atoms
> 6 MainChain+Cb : 1206 atoms
> 7 MainChain+H : 1198 atoms
> 8 SideChain : 2650 atoms
> 9 SideChain-H : 1006 atoms
> 10 Prot-Masses : 3848 atoms
> 11 Non-Protein : 33922 atoms
> 12 LIG : 35 atoms
> 13 SOL : 33807 atoms
> 14 Na : 46 atoms
> 15 Cl : 34 atoms
> 16 Other : 33922 atoms
>
> nr : group ! 'name' nr name 'splitch' nr Enter: list groups
> 'a': atom & 'del' nr 'splitres' nr 'l': list residues
> 't': atom type | 'keep' nr 'splitat' nr 'h': help
> 'r': residue 'res' nr 'chain' char
> "name": group 'case': case sensitive 'q': save and quit
>
>> 12 & 1
>
> Copied index group 12 'LIG'
> Copied index group 1 'Protein'
> Merged two groups with AND: 35 3848 -> 0
> Group is empty
>
>> 1 & 12
>
> Copied index group 1 'Protein'
> Copied index group 12 'LIG'
> Merged two groups with AND: 3848 35 -> 0
> Group is empty
>
The use of & tells make_ndx to write out a group that is the intersection of
these two. If there are no overlaps, the group is empty. What you want is the
"or" operator:
12 | 1
-Justin
>
>
>
> On Sat, May 22, 2010 at 9:57 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> John Shultz wrote:
>>> Justin,
>>>
>>> I finally got a chance to get back to this. I read the make_ndx
>>> instructions. Unless I am mistaken, I guess that is what you use to
>>> merge groups.
>>>
>> Yep, that's the purpose of make_ndx.
>>
>> -Justin
>>
>>> Thanks,
>>>
>>> Jack
>>>
>>> On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>> John Shultz wrote:
>>>>> Thank you Justin, is there a way I can choose both Protein LIG? It has
>>>>> the following options for me
>>>>>
>>>> You need to make a custom group that merges these two.
>>>>
>>>> -Justin
>>>>
>>>>> Reading toplogy and shit from md.tpr
>>>>> Reading file md.tpr, VERSION 4.0.5 (single precision)
>>>>> 50000 steps (100 ps) remaining from first run.
>>>>> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
>>>>> Group 0 ( System) has 37770 elements
>>>>> Group 1 ( Protein) has 3848 elements
>>>>> Group 2 ( Protein-H) has 1980 elements
>>>>> Group 3 ( C-alpha) has 244 elements
>>>>> Group 4 ( Backbone) has 732 elements
>>>>> Group 5 ( MainChain) has 974 elements
>>>>> Group 6 (MainChain+Cb) has 1206 elements
>>>>> Group 7 ( MainChain+H) has 1198 elements
>>>>> Group 8 ( SideChain) has 2650 elements
>>>>> Group 9 ( SideChain-H) has 1006 elements
>>>>> Group 10 ( Prot-Masses) has 3848 elements
>>>>> Group 11 ( Non-Protein) has 33922 elements
>>>>> Group 12 ( LIG) has 35 elements
>>>>> Group 13 ( SOL) has 33807 elements
>>>>> Group 14 ( Na) has 46 elements
>>>>> Group 15 ( Cl) has 34 elements
>>>>> Group 16 ( Other) has 33922 elements
>>>>> Select a group:
>>>>>
>>>>>
>>>>> On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>> John Shultz wrote:
>>>>>>> I am trying to rerun a simulation using this command
>>>>>>> mdrun -rerun -v -deffnm md
>>>>>>>
>>>>>>> I think I must have made a mistake when I prepared the original mdp
>>>>>>> file because I get this message
>>>>>>> Number of atoms in trajectory (3883) does not match the run input file
>>>>>>> (37770)
>>>>>>>
>>>>>>> I have these files in my directory
>>>>>>> Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp
>>>>>>> md_prev.cpt md.tpr md.trr md.xtc traj.trr
>>>>>>>
>>>>>>> Here is my mdp file, should I remove entries for xtc_grps and
>>>>>>> energygrps to avoid this issue?
>>>>>>>
>>>>>> You can, but it won't fix anything. Your original .xtc file saved only
>>>>>> the
>>>>>> coordinates of the Protein and LIG (per your output options), but your
>>>>>> .tpr
>>>>>> file has all of these atoms, regardless of what you choose to save.
>>>>>> You
>>>>>> can, however, create a .tpr file that has a just these atoms by passing
>>>>>> your
>>>>>> original .tpr file to tpbconv, using a suitable index group.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>> integrator = md
>>>>>>> nsteps = 50000
>>>>>>> dt = 0.002
>>>>>>> nstvout = 5000
>>>>>>> nstlog = 500
>>>>>>> nstenergy = 250
>>>>>>> nstxtcout = 5000
>>>>>>> nstxout = 5000
>>>>>>> xtc_grps = Protein LIG
>>>>>>> energygrps = Protein SOL
>>>>>>> constraints = all-bonds
>>>>>>> nstcomm = 1
>>>>>>> ns_type = grid
>>>>>>> rlist = 1.2
>>>>>>> rcoulomb = 1.1
>>>>>>> rvdw = 1.0
>>>>>>> vdwtype = shift
>>>>>>> rvdw-switch = 0.9
>>>>>>> coulombtype = PME-Switch
>>>>>>> Tcoupl = v-rescale
>>>>>>> tau_t = 0.1 0.1
>>>>>>> tc-grps = protein non-protein
>>>>>>> ref_t = 300 300
>>>>>>> Pcoupl = parrinello-rahman
>>>>>>> PcOupltype = isotropic
>>>>>>> tau_p = 0.5
>>>>>>> compressibility = 4.5e-5
>>>>>>> ref_p = 1.0
>>>>>>> gen_vel = yes
>>>>>>> lincs-iter = 2
>>>>>>> DispCorr = EnerPres
>>>>>>> optimize_fft = yes
>>>>>>> gen_seed = 805087
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> MILES-IGERT Trainee
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>
>>>>>> ========================================
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> 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/search before posting!
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>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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