[gmx-users] confout.gro

Tue Jul 8 10:04:11 CEST 2014

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
>
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