It is fine. My question was not about '.mdp' itself. I meant how to define the 'Temperature' inside the bash scrip, to avoid changing it by opening the .mdp file.
On Thu, Mar 7, 2019 at 4:57 PM Quyen Vu <[email protected]> wrote: > Dear all, > It's my fault that I have un-nice behavior, I'm so sorry for that. > If I understand correctly, you are working with Gromacs so you should > understand what is the .mdp file used for and there, the document of > temperature section talk about that. > > > On Thu, Mar 7, 2019 at 4:06 PM Amin Rouy <[email protected]> wrote: > > > Thank you Justin. > > > > Yes, Quyen I've read the manual. I got helps from Justin's scrips in his > > tutorial page (great source) and googled before I came to write here. > > > > > > On Thu, Mar 7, 2019 at 4:01 PM Justin Lemkul <[email protected]> wrote: > > > > > > > > > > > On 3/7/19 9:56 AM, Quyen Vu wrote: > > > > my question for you: have you ever read gromacs manual/documentation? > > > > > > Where in the GROMACS manual do we discuss how to use Linux commands to > > > alter scripts in this way? Please do not simply dismiss others' > > > questions; it is not productive and not helpful. There are legitimate > > > cases of users not utilizing documentation and web searching, but I > > > would argue this is not one of them. > > > > > > > On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy <[email protected]> > > wrote: > > > > > > > >> Hi > > > >> > > > >> I would like to change the temperature of the simulation (NPT.mdp) > > > inside > > > >> my bash script, any one has idea? > > > > > > You can make replacements in files using standard Linux utilities like > > > sed, in conjunction with others like grep and awk. This isn't a > > > GROMACS-specific issue, so I'd suggest looking at more general Linux > > > forums. > > > > > > -Justin > > > > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Assistant Professor > > > Office: 301 Fralin Hall > > > Lab: 303 Engel Hall > > > > > > Virginia Tech Department of Biochemistry > > > 340 West Campus Dr. > > > Blacksburg, VA 24061 > > > > > > [email protected] | (540) 231-3129 > > > http://www.thelemkullab.com > > > > > > ================================================== > > > > > > -- > > > 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 [email protected]. > > > > > -- > > 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 [email protected]. > > > -- > 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 [email protected]. > -- 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 [email protected].
