[gmx-users] confout.gro

Tue Jul 8 12:16:49 CEST 2014

hello every one
now i am using command

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr -maxwarn
mdrun -deffnm em
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat

 so i have to follow all four command again and again or any thing
else i am using second third and fourth command but all time result is
same

help

On Tue, Jul 8, 2014 at 1:34 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello gromacs users
> ok justin i am going back now i am generating all the files but still
> confusion
>
> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
>
> i used this step after this
>
> trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact
>
> after this
>
> editconf -f KALP_processed.gro -o KALP_newbox.gro -c -box 6.41840 6.44350 6.59650
>
> cat KALP_newbox.gro dppc128_whole.gro > system.gro
>
> genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
>
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
>
> then mdrun -v deffnum em
>
> then
>
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
>  and
>
> mdrun -v deffnum em
>
> is it ok aur change the file no
>
> help
>
>
>
>
>
>
>
>
> On Mon, Jul 7, 2014 at 5:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/7/14, 6:34 AM, RINU KHATTRI wrote:
>>
>>> hello
>>>
>>> the command is gmx grompp when i am running
>>> gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
>>> No command 'gmx' found, did you mean:
>>>   Command 'gm' from package 'graphicsmagick' (universe)
>>>   Command 'pmx' from package 'pmx' (universe)
>>>   Command 'ngmx' from package 'gromacs' (universe)
>>>   Command 'gcx' from package 'gcx' (universe)
>>> gmx: command not found
>>> mtechbio at mtechbio-HP-Z400-Workstation:~/Desktop/fresh1$ gmx  grompp -f
>>> ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
>>> No command 'gmx' found, did you mean:
>>>   Command 'gm' from package 'graphicsmagick' (universe)
>>>   Command 'pmx' from package 'pmx' (universe)
>>>   Command 'ngmx' from package 'gromacs' (universe)
>>>   Command 'gcx' from package 'gcx' (universe)
>>> gmx: command not found
>>> help
>>>
>>>
>> As announced this morning, I am upgrading the tutorials to be compatible
>> with Gromacs version 5.0, so the syntax of commands is slightly different.
>>  Leave off "gmx" if you're using an older version.
>>
>> -Justin
>>
>>
>>
>>> On Mon, Jul 7, 2014 at 3:47 PM, RINU KHATTRI <nickname.mittu at gmail.com>
>>> wrote:
>>>
>>>  hello gmx users
>>>> i am also getting that error
>>>> [file topol.top, line 24832]:
>>>>    System has non-zero total charge: 14.788998
>>>>    Total charge should normally be an integer. See
>>>>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>>>>    for discussion on how close it should be to an integer
>>>>
>>>>
>>>> On Mon, Jul 7, 2014 at 2:47 PM, RINU KHATTRI <nickname.mittu at gmail.com>
>>>> wrote:
>>>>
>>>>  hello gromacs users
>>>>> i am applying (solv.gro 101917-108573 topol.top )/3
>>>>> =     i have to subtract 2218.66 into old figure (32672 which is
>>>>> present
>>>>> in topol.top )
>>>>> due to float no still error persist only one coordinate is different
>>>>> Fatal error:
>>>>> number of coordinates in coordinate file (solv.gro, 101917)
>>>>>               does not match topology (topol.top, 101916)
>>>>> how to resolve
>>>>> i have been apply all the numbers in float but still difference
>>>>> help
>>>>>
>>>>>
>>>>> On Mon, Jul 7, 2014 at 2:06 PM, RINU KHATTRI <nickname.mittu at gmail.com
>>>>> >
>>>>> wrote:
>>>>>
>>>>>  hello everyone
>>>>>> after this step now i am in the
>>>>>>   grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
>>>>>> step but after running i got error
>>>>>> Fatal error:
>>>>>> number of coordinates in coordinate file (solv.gro, 101917)  does not
>>>>>> match topology (topol.top, 604599)
>>>>>> i have been edited the sol (counted from solv.gro) but still error how
>>>>>> to resolve it infact figure is increased
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Jul 7, 2014 at 12:05 PM, RINU KHATTRI <
>>>>>> nickname.mittu at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>  hello gromacs users
>>>>>>> thanks justin i have applied
>>>>>>>
>>>>>>> perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5
>>>>>>> area.dat
>>>>>>>
>>>>>>> mdrun -v -deffnm em
>>>>>>>
>>>>>>> perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
>>>>>>> area_shrink1.dat
>>>>>>>
>>>>>>> after that solvation step but no command is present in dppc tutorial
>>>>>>> should i used
>>>>>>>
>>>>>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>>>>>>
>>>>>>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>>>>>>
>>>>>>> but conf.gro is the combined file of (b3_procesed.gro+ drg.itp)
>>>>>>>
>>>>>>> is it this file or em.gro which is formed 2 step before this
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Jul 5, 2014 at 4:11 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> On 7/5/14, 12:51 AM, RINU KHATTRI wrote:
>>>>>>>>
>>>>>>>>  hello gromacs users
>>>>>>>>> but i am confussed if confout.gro is input, in which step it is
>>>>>>>>> formed
>>>>>>>>> according to tutorial before this step the step is
>>>>>>>>> perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5
>>>>>>>>> area.dat
>>>>>>>>> is system_inflated.gro is confout.gro or which gro file i must be
>>>>>>>>> used
>>>>>>>>> as confout.gro
>>>>>>>>>
>>>>>>>>> perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5
>>>>>>>>> area_shrink1.dat
>>>>>>>>>
>>>>>>>>>
>>>>>>>> The file "confout.gro" is the default name of the final output
>>>>>>>> coordinates of an mdrun process, unless you provide a different
>>>>>>>> file name
>>>>>>>> to mdrun -c.  In this case, the protocol is:
>>>>>>>>
>>>>>>>> 1. Inflate the system (produce system_inflated.gro)
>>>>>>>> 2. Minimize the inflated system (produce confout.gro, unless
>>>>>>>> otherwise
>>>>>>>> named)
>>>>>>>> 3. Begin shrinking the system, starting with the output of step 2.
>>>>>>>>
>>>>>>>> So "confout.gro" is the _output_ of step 2 and the _input_ of step
>>>>>>>> 3.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>> --
>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>>>
>>>>>>>> Department of Pharmaceutical Sciences
>>>>>>>> School of Pharmacy
>>>>>>>> Health Sciences Facility II, Room 601
>>>>>>>> University of Maryland, Baltimore
>>>>>>>> 20 Penn St.
>>>>>>>> Baltimore, MD 21201
>>>>>>>>
>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>>
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>
>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>
>>>>>>>> * For (un)subscribe requests visit
>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>> or
>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>>
>
>