[gmx-users] rerun trajectory does not match input file
John Shultz
jackygrahamez at gmail.com
Sat May 22 16:31:30 CEST 2010
Thanks Justin!
On Sat, May 22, 2010 at 10:12 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> 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!
>>>>> 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/mailing_lists/users.php
>>>>>
>>> --
>>> ========================================
>>>
>>> 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!
>>> 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/mailing_lists/users.php
>>>
>>
>
> --
> ========================================
>
> 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!
> 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/mailing_lists/users.php
>
More information about the gromacs.org_gmx-users
mailing list