Re: [gmx-users] script
You could use a sed command in your script to replace that line, something like sed "s/original expression/new expression/" filename -i But it depends a lot on how your mdp file is formatted in terms of spaces and tabs. Hope it helps, On Thu, 7 Mar 2019, 12:14 Amin Rouy, wrote: > Hi > > I would like to change the temperature of the simulation (NPT.mdp) inside > my bash script, any one has idea? > thanks > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
Re: [gmx-users] script
a dirty way: grep -v ref_t npt.mdp >new.mdp && echo -e "ref_t=300" >>new.mdp sorry again! On Thu, Mar 7, 2019 at 6:16 PM Amin Rouy wrote: > 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 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 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 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 > > > 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 > > > > > > > > jalem...@vt.edu | (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 gmx-users-requ...@gromacs.org. > > > > > > > -- > > > 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-requ...@gromacs.org. > > > > > -- > > 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-requ...@gromacs.org. > > > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
Re: [gmx-users] script
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 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 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 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 > > 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 > > > > > > jalem...@vt.edu | (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 gmx-users-requ...@gromacs.org. > > > > > -- > > 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-requ...@gromacs.org. > > > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
[gmx-users] VMD visualization is failed
Dear all I have simulated a protein-ligand system and the md.xtc and md.gro are now generated in the output. Unlike my previous simulations of nano systems in which the .trr trajectory was in the output and the visualization could be done in an straight forward way of opening the .gro and .trr consecutively, the .trr is not present now. I used gmx_mpi -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr AND gmx_mpi mdrun -ntomp 2 -pin auto -s md.tpr -cpi md.cpt -tunepme -v -gpu_id 0 -nb gpu AND also gmx_mpi trjconv -f md.xtc -s md.tpr -o md_convert.gro -ur compact -pbc mol -center. How should I visualize the simulation in VMD having the .gro and .xtc?Is there a problem in the commands I used or a missing option in the .mdp that the .trr is not generated?Thanks. -- 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-requ...@gromacs.org.
[gmx-users] User tabulated potential and VdW Modifier
Dear everyone, My question concerns the effect of the mdp option "vdw-modifier" when vdwtype is set to user. I have a tabulated 8 - 6 Mie potential and I'm simulating a coarse grained water, NaCl system, which all interact with the same potential form but different dispersion coefficients. I wanted to check the energy conservation of that system and therefore set up a simulation as follows: dt = 0.008 cutoff-scheme = group rlist = 2.3 vdwtype = user vdw-modifier = potential-shift rvdw = 2 rvdw-switch = 2 coulomtype = PME-switch rcoulomb = 2 rcoulomb-switch = 1.95 I will limit my discussion to the VdW energies, since I trust the PME algorithm and I did not change any of the settings in the following discussion. As far as I can judge, this system should be energy conserving, because the potential is shifted, and there is enough space between rvdw and rlist to allow for diffusion in between updates of the neighbourlist. However, this system exhibits an energy drift (total energy) of over 1000 kJ/mol over the course of 30.000 integration steps. On a side note, I also calculated the LJ long range corrections, which is -1888 kJ/mol. After this simulation I thought, that the vdw-modifier does not affect the tabulated potential. Therefore, I calculated a shifted version of my potential and fed it to gromacs with the same parameters except: vdw-modifier = none which effectively should enforce a cutoff equal to that in my tabulated potential (2nm). This setup conserves the energy (Drift ~ 0.4 kJ/mol) and gives me a slightly higher LJ energy, which I expected. However, the long range correction was different: -946 kJ/mol (appr. half). This seemed odd to me, so I played around with some settings and found that the LR correction took the value of -946 for vdw-modifier = none and -1888 for vdw-modifier = potential-shift. This was also true for a setup with rlist = rvdw = rvdw-switch = 2 (and nstlist = 1), so it wasn't the difference between rlist and rvdw-switch. According to the manual and grompp notes, the LR correction is calculated as -C6/r_c^6, which should be the same for all simulations, but apparently the vdw-modifier changes something somewhere. Does anyone have an explanation on what's the reason for the behaviour of the LR correction? And also, more generally, are vdw modifier supposed to work for user lists (and if so, why did my initial setup not work)? Thank you very much in advance, Matthias -- 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-requ...@gromacs.org.
Re: [gmx-users] script
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 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 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 > 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 > > > > jalem...@vt.edu | (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 gmx-users-requ...@gromacs.org. > > > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
Re: [gmx-users] script
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 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 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 > > jalem...@vt.edu | (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 gmx-users-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
Re: [gmx-users] script
This is a welcoming and friendly community, with somewhat busy but still nice people. The manual is available at: http://manual.gromacs.org/documentation/ One can search for temperature information here: http://manual.gromacs.org/documentation/current/reference-manual/index.html to find : http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=temperature On 3/7/19 4:56 PM, Quyen Vu wrote: my question for you: have you ever read gromacs manual/documentation? On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy wrote: Hi I would like to change the temperature of the simulation (NPT.mdp) inside my bash script, any one has idea? thanks -- 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.
Re: [gmx-users] script
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 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 jalem...@vt.edu | (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 gmx-users-requ...@gromacs.org.
Re: [gmx-users] script
my question for you: have you ever read gromacs manual/documentation? On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy wrote: > Hi > > I would like to change the temperature of the simulation (NPT.mdp) inside > my bash script, any one has idea? > thanks > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.
[gmx-users] question about the QM/MM calcuation in Gromacs/ORCA interface
Dear all, I am going to use Gromacs/ORCA interface for QM/MM calculation in the metalloenzyme model. I have done some QMMM calculations with other interface (AMBER/TURBOMOLE) I am also familiar with QM in ORCA but new user of Gromacs! I could get general overview how this feature works in Gromacs (from 2 provided tutorial examples and also Q/A of users in the mailing list) but that would be great to have a successful sample model to reproduce data before running the real model. I was going to test "Thymine dimer splitting" as given example with MOPAC interface (http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/tutorial.html) and using provided files from the website then use ORCA interface for QM part but it was not successful. so can you please someone share the example with me (inputs/output). Any help would be really appreciated! Regards, Zahra -- Zahra Aliakbar Tehrani Ph.D. in Physical Organic Chemistry Post-Doctoral Researcher, Institute of Organic Chemistry & Biochemistry AS CR, v.v.i. (IOCB), 166 10 Praha 6 E-mail: zahra.aliakbar_tehr...@uochb.cas.cz -- 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-requ...@gromacs.org.
[gmx-users] script
Hi I would like to change the temperature of the simulation (NPT.mdp) inside my bash script, any one has idea? thanks -- 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-requ...@gromacs.org.
[gmx-users] v-rescale reproducible restart
Dear gmx comunity, I have done the following: -Ran a 100ps simulation and then starting with the same conditions a 30ps simulation and then restarted upto 100ps. -If I use -reprod and Nosé hoover thermostat in both trajectories the final structures match. -If I use v-rescale it doesn't. I know since v-rescale is stocastic, random numbers should be properly saved in the cpt for the chain of random numbers to be reproducible when doing a restart. I am not sure if this is not happening because it is impossible to do or if it is a bug. If it is not a bug, a note or something in this regard in the output would be nice. I am using gromacs.2018.4 with mpi. In addition, I think the name of the thermostat "v-rescale" is not very good (although I am not sure if it's too late to be changed). It gives the impression that velocities are just being rescaled (which would be completely wrong). Furthermore, if we credit with the author name the Parrinello-Rahman, Nose-Hoover, Berendsen methods. Why not Bussi-Donaio-Parrinello? Thank you very much! Sergio Pérez-Conesa -- 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-requ...@gromacs.org.
