[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5?
qiancheng shen
qianchengshen at gmail.com
Sun Mar 18 11:20:48 CET 2012
Dear David,
Thank you very much!!
Your suggestion works!! After removing water and ion from my
structure, I did normal mode analysis successfully!!
I appreciate your help.
Shen
在 2012年3月17日 下午11:45，Justin A. Lemkul <jalemkul at vt.edu>写道：
>
>
> qiancheng shen wrote:
>
>> Dear David,
>> Thank you very much.
>> /* A little modification to your first post. */
>>
>> "
>> grompp_d -f cg -o cg
>> mdrun_d -s cg/* -o*/ conf.g96 --------------------->
>> mdrun_d -s cg /*-c*/ conf.g96 (Use -o will only output *.trr)
>>
>> grompp_d -f nm -c conf.g96 -o nm
>> mdrun_d -s nm
>> g_nmeig_d
>> "
>> And when I used "integrator = nm" in *.mdp file and run "mdrun_d -s
>> nm". Gromacs said "Constraints present with Normal Mode Analysis, this
>> combination is not supported".
>> Could give me some suggestion about that error?
>> The commands I used is listed below:
>> 1. */pdb2gmx_d -ignh -ff /*/gromos43a1 *-f* 1OMB.pdb *-water* spce
>> *-o* conf.gro *-p* topol.top/
>> 2. *///editconf_d -f /*/conf.gro *-o* BOX.gro *-d* 1.5/
>> 3. */genbox_d -cp /*/BOX.gro *-cs* spc216 *-o* SOL *-p* topol.top/
>> 4. */grompp_d -f /*/em.mdp *-c* SOL.gro *-p* topol.top *-o* em.tpr/
>> 5. */mdrun_d -s /*/em.tpr *-deffnm* em *-c* tx.g96 *-v*/ //Energy
>> Min
>> 6. /*grompp_d*/ /*-f */nm.mdp /*-c*/ tx.g96 /*-o*/ nm
>> 7. /*mdrun_d*/ /*-s*/ nm -----> A fatal error "Constraints present
>> with Normal Mode Analysis, this combination is not supported"
>>
>>
> In adding solvent, these molecules are held rigid by the SETTLE algorithm,
> which is a type of constraint. As the fatal error tells you, you cannot do
> this. See below for more comments on em.mdp.
>
> /*em.mdp*/
>>
>> define = -DFLEXIBLE
>> constraints = none
>> integrator = steep
>> dt = 0.002 ; ps !
>> nsteps = 400
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.0
>> coulombtype = PME
>> rcoulomb = 1.0
>> vdwtype = cut-off
>> rvdw = 1.4
>> optimize_fft = yes
>> ;
>> ; Energy minimizing stuff
>> ;
>> emtol = 1000
>> emstep = 0.01
>>
>>
> Steepest descents EM with this large of a maximum force is not appropriate
> for running NM calculations. You need extremely thorough EM, perhaps
> several rounds of it using either CG or L-BFGS (or both) to a maximal force
> as low as machine precision will allow.
>
> -Justin
>
> ------------------------------**---------
>> /*nm.mdp*/
>>
>> constraints = none
>> integrator = nm
>> dt = 0.002 ; ps !
>> nsteps = 400
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.2
>> coulombtype = PME-Switch
>> rcoulomb = 1.0
>> vdwtype = Cut-off
>> rvdw = 1.4
>>
>>
>> Thank you very much.
>>
>> Shen.
>>
>> 在 2012年3月17日 下午10:46，David van der Spoel <spoel at xray.bmc.uu.se <mailto:
>> spoel at xray.bmc.uu.se>>**写道：
>>
>>
>> On 2012-03-17 15:34, qiancheng shen wrote:
>>
>> Dear David:
>> Thank you very much!! I'm really new to Gromacs.
>> I think I should use the *.trr file(from mdrun_d, energy
>> minimization)
>> as an input file for generating *.tpr for Normal Mode Analysis.
>>
>>
>> Please read my previous email.
>>
>>
>> But what the *.mdp file looks like while using "grompp_d -f nm -c
>> conf.g96 -o nm" to make such *.tpr file?
>>
>> integrator = nm
>>
>> I appreciate your help.
>>
>> Shen
>>
>> 在 2012年3月17日 下午9:47，David van der Spoel
>> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>**
>> >__写道：
>>
>>
>>
>> On 2012-03-17 14:44, qiancheng shen wrote:
>>
>> Hello Everyone，
>> I‘m confused about Normal Mode Analysis of Gromacs. I have
>> googled a lot
>> but find little useful.
>> I installed Gromacs 4.5.5 by CMake on Win7(Double
>> Precision).
>> Gromacs manual said "It is imperative that you use the |-t|
>> option to
>> |grompp
>> <http://www.gromacs.org/____**
>> Documentation/Gromacs_____**Utilities/grompp<http://www.gromacs.org/____Documentation/Gromacs_____Utilities/grompp>
>> <http://www.gromacs.org/__**Documentation/Gromacs___**
>> Utilities/grompp<http://www.gromacs.org/__Documentation/Gromacs___Utilities/grompp>
>> >
>>
>>
>> <http://www.gromacs.org/__**Documentation/Gromacs___
>> **Utilities/grompp<http://www.gromacs.org/__Documentation/Gromacs___Utilities/grompp>
>> <http://www.gromacs.org/**Documentation/Gromacs_**Utilities/grompp<http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp>
>> >>>|
>>
>> when you create the normal mode run input file
>> <http://www.gromacs.org/____**
>> Documentation/File_Formats/___**_Topology_%28.tpr%29_File<http://www.gromacs.org/____Documentation/File_Formats/____Topology_%28.tpr%29_File>
>> <http://www.gromacs.org/__**Documentation/File_Formats/__**
>> Topology_%28.tpr%29_File<http://www.gromacs.org/__Documentation/File_Formats/__Topology_%28.tpr%29_File>
>> >
>>
>>
>> <http://www.gromacs.org/__**
>> Documentation/File_Formats/__**Topology_%28.tpr%29_File<http://www.gromacs.org/__Documentation/File_Formats/__Topology_%28.tpr%29_File>
>> <http://www.gromacs.org/**Documentation/File_Formats/**
>> Topology_%28.tpr%29_File<http://www.gromacs.org/Documentation/File_Formats/Topology_%28.tpr%29_File>
>> >>>,
>>
>> so that you read full precision binary coordinates and
>> not the
>> three-decimal .gro
>> <http://www.gromacs.org/____**
>> Documentation/File_Formats/.__**__gro_File<http://www.gromacs.org/____Documentation/File_Formats/.____gro_File>
>> <http://www.gromacs.org/__**Documentation/File_Formats/.__**
>> gro_File<http://www.gromacs.org/__Documentation/File_Formats/.__gro_File>
>> >
>>
>>
>> <http://www.gromacs.org/__**
>> Documentation/File_Formats/.__**gro_File<http://www.gromacs.org/__Documentation/File_Formats/.__gro_File>
>> <http://www.gromacs.org/**Documentation/File_Formats/.**gro_File<http://www.gromacs.org/Documentation/File_Formats/.gro_File>
>> >>>
>> file." But
>>
>> I don't exactly what it means....
>> Could anyone give me a step-by-step example?
>>
>> Thanks in advance.
>>
>> shen
>>
>>
>> grompp_d -f cg -o cg
>> mdrun_d -s cg -o conf.g96
>> grompp_d -f nm -c conf.g96 -o nm
>> mdrun_d -s nm
>> g_nmeig_d
>>
>> You can use the g96 coordinate format instead of using the
>> trr file
>> from the conjugate gradients energy minimization.
>> Set all cut-offs to zero (= infinite).
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
>>
>>
>> http://folding.bmc.uu.se
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>>
>> -- David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>> http://folding.bmc.uu.se
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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