[gmx-users] rerun trajectory does not match input file
John Shultz
jackygrahamez at gmail.com
Sat May 22 16:11:06 CEST 2010
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
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
>
More information about the gromacs.org_gmx-users
mailing list