Re: [gmx-users] DSSP graph re-scale

[Mohammadreza Niknam Hamidabad]

Dear Syah,

the answer depends on the way you're creating .eps file. I'm assuming that
you're using the gmx do_dssp then gmx xpm2ps.
something like this can be used:

gmx do_dssp -f final.xtc -s my.tpr -n new.ndx -map first.map -tu ns -b 700
-e 1000 -o protein.xpm

gmx xpm2ps -f protein.xpm -di scale.m2p -title top -bx 8.0 -by 50 -o
sec_struc_new.eps

if the x-axis ticks is the problem, you can change the font or anything
related to it, in the .m2p file. (
http://manual.gromacs.org/archive/5.0.3/online/m2p.html)
I hope you find it useful.

Best regards,
Mohammadreza Niknam Hamidabad


On Tue, Sep 10, 2019 at 6:18 AM SGR160055 Student 
wrote:

> Dear experts,
>
> I have an issue to re-scale the x-axis on DSSP graph eps format for my 100
> ns simulation time.
>
> The x-axis of the graph became too compact until it can't be read clearly.
>
> How should I solve this? Is there anyway to re-scale the graph for eps
> format.
>
> Your help is much appreciated. Thank you.
>
>
>
> Regards,
> Syah
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Re: [gmx-users] regarding changing the scale from ps to ns

[Mohammadreza Niknam Hamidabad]

Hi,
I'm currently using Gromacs 2018 and I'm not quite sure about the 5.x
version. The gyrate module doesn't have -tu flag so my suggestion is that
you convert your .xtc file to a new xtc file with trjconv -tu ns then use
gyrate for your calculation.
I hope you find it useful.

Best regards,
Reza


On Thu, Aug 29, 2019 at 7:38 AM sudha bhagwati 
wrote:

> Hi,
>
> I am using the GROAMCS 5.1.4 version.
>
> 
> Running the commands below:
>
>
> *gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns*
> *OR*
> *gmx energy -f ie.edr -o interaction_energy.xvg -tu ns*
>
>
> Error while executing commands:
>
> *Error in user input:*
>
> *Invalid command-line optionsUnknown command-line option -tu*
>
> 
>
> I want to generate my plots for nanosecond scale. Could you please help me
> out with this issue. I'd be really grateful to you.
>
> Thank you.
>
>
> --
> Thanks & regards
> ~
> Sudha Bhagwati
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Re: [gmx-users] [gmx-user] Parameter files for Lysozyme in water tutorial - Charmm36

[Mohammadreza Niknam Hamidabad]

Hi,
The parameters you should use for CHARMM36 are provided here (As you
mentioned in your mail):
<
http://manual.gromacs.org/documentation/2018/user-guide/force-fields.html#targetText=CHARMM%20(Chemistry%20at%20HARvard%20Macromolecular,CHARMM27%2C%20CHARMM36)%20force%20fields
>
If you encounter some errors please, copy-paste them in your email and the
commands you used.
Besides, if you use the charmm36 you can use CHARMM-GUI. In your case, you
should probably use the solution builder:
Solution Builder 
When you provide all the inputs and parameters, you can download the final
files (including all the *.mdp files)
I hope you find it useful.

Best regards,
Reza


On Wed, Aug 28, 2019 at 1:22 PM Quin K  wrote:

> Hi
>
> Does anyone have *.mdp* files for Lysozyme in water (With CHARMM36 FF)
> tutorial given in following link.
> http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html
> I want to try this for a project I'm doing.
> There are 4 .mdp files
> ions.mdp 
> minim.mdp 
> nvt.mdp
> npt.mdp 
>
> I have tried to change the parameter files for CHARMM36 but did not
> succeed.
> CHARRM36
> <
> http://manual.gromacs.org/documentation/2018/user-guide/force-fields.html#targetText=CHARMM%20(Chemistry%20at%20HARvard%20Macromolecular,CHARMM27%2C%20CHARMM36)%20force%20fields
> >
> Thank you in advance!!
>
> Regards!
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Re: [gmx-users] continue run

[Mohammadreza Niknam Hamidabad]

Hi,
you can generate a new .tpr file by extend flag ( time is in ps) then run
your code again. Please replace the names carefully. Also, check this link :

http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-convert-tpr.html

gmx convert-tpr -s last.tpr -o new.tpr -extend 1

gmx mdrun -v -deffnm new -cpi last.cpt -noappend

Best regards,
Mohammadreza Niknam Hamidabad


On Fri, Aug 16, 2019 at 12:09 PM Dhrubajyoti Maji  wrote:

> Hi all,
>I have a simulated trajectory of 50 ns but my desired property is not
> well converged. Therefore, I want to extend the run for another 50 ns. As
> far as I know if I use the last output files as input files for next run, I
> can finally have two 50 ns run trajectory files. But if I want a 100 ns
> trajectory then what should I do? Any kind of help will be highly
> appreciated.
> Thanks and regards.
> Dhrubajyoti Maji
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