[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5?
qiancheng shen
qianchengshen at gmail.com
Sat Mar 17 16:33:02 CET 2012
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 -oconf.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"
*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
---------------------------------------
*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>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>>**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>
>> >>|
>>
>> 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>
>> >>,
>>
>> 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>
>> >>
>> 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>
>>
>> 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 http://folding.bmc.uu.se
> --
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