Re: [gmx-users] Freeze group atoms changing position
Just as an update, I ran the simulation using position restraints with force constants set to 1 for each atom in the restrained waters, and none jumped out of the nanotube. Thanks for the help! On Thu, Nov 1, 2012 at 5:01 PM, Justin Lemkul wrote: > > > On 11/1/12 4:56 PM, Alex Marshall wrote: > >> I've created a position restraint file for the specific waters that I need >> to immobilize, but I'm having a hard time getting grompp to apply it >> successfully. No matter where I put #include "posre.itp" in my topology >> file grompp returns fatal errors about the atomic indices being out of >> bounds. Is it actually possible to only apply position restraints to some >> molecules within a species and leave the rest alone? >> >> > Yes, but you can't simply #include "spc.itp" and then call the position > restraint file, for example. You need a [moleculetype] for the entire > block of water, since position restraints can only be applied per > [moleculetype]. > > -Justin > > On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul wrote: >> >> >>> >>> On 10/31/12 3:55 PM, Alex Marshall wrote: >>> >>> Chris, is that for freeze groups or position restraints? >>>> >>>> >>>> I will assume Chris was referring to the restraint method - you need an >>> index file for creating the position restraint .itp file using genrestr. >>> It will save you a ton of time over doing it manually. >>> >>> -Justin >>> >>> >>> On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale < >>> >>>> chris.ne...@mail.utoronto.ca> wrote: >>>> >>>> No need to rename... just make an .ndx group. >>>> >>>>> >>>>> -- original message -- >>>>> >>>>> As I understand it, position restraints for an atom are set in the >>>>> topology >>>>> file and applied to that atom in each of that species. In order to >>>>> restrain >>>>> some but not all of the water I'd have to copy the topology of my water >>>>> model and add the restraints, then rename (and group together) the >>>>> atoms >>>>> I >>>>> want to freeze so that they're identified with the appropriate topology >>>>> file. Does this sound like it would work? Is there some other way that >>>>> you >>>>> might do it? >>>>> >>>>> Thanks >>>>> >>>>> On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall >>>>> wrote: >>>>> >>>>> Justin: I'll try using position restraints instead of freezing the >>>>> water >>>>> >>>>>> in the tube. Thanks for the tip. >>>>>> >>>>>> Bogdan: I don't think I'm using constraints other than freeze groups. >>>>>> I >>>>>> wasn't using energy group exclusions though. I tried running the >>>>>> >>>>>> simulation >>>>> >>>>> from the same initial configuration with newly-defined energy groups >>>>>> CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second >>>>>> for >>>>>> the free atoms. The list of exclusions reads: >>>>>> energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN >>>>>> >>>>>> Long story short, I'm roughly 15 ns into the simulation and the same >>>>>> two >>>>>> waters have jumped. I'll check the manual again though. Thanks. >>>>>> >>>>>> On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu >>>>> >>>>>> gmail.com>wrote: >>>>> >>>>> >>>>>> On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall >>>>>> >>>>>>> >>>>>>> wrote: >>>>>> >>>>> >>>>> Thanks Justin. I identified the offending waters using vmd (adding 1 >>>>>> >>>>>>> >>>>>>>> to >>>>>>> >>>>>> >>>>> resID and atom number since vmd starts counting at 0) and checked >>>>>> >>>>>>> confout.gro to make sure the coordinates matched up. I only have one >>>>>>>> >>>>>>>>
Re: [gmx-users] Freeze group atoms changing position
I've created a position restraint file for the specific waters that I need to immobilize, but I'm having a hard time getting grompp to apply it successfully. No matter where I put #include "posre.itp" in my topology file grompp returns fatal errors about the atomic indices being out of bounds. Is it actually possible to only apply position restraints to some molecules within a species and leave the rest alone? On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul wrote: > > > On 10/31/12 3:55 PM, Alex Marshall wrote: > >> Chris, is that for freeze groups or position restraints? >> >> > I will assume Chris was referring to the restraint method - you need an > index file for creating the position restraint .itp file using genrestr. > It will save you a ton of time over doing it manually. > > -Justin > > > On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale < >> chris.ne...@mail.utoronto.ca> wrote: >> >> No need to rename... just make an .ndx group. >>> >>> -- original message -- >>> >>> As I understand it, position restraints for an atom are set in the >>> topology >>> file and applied to that atom in each of that species. In order to >>> restrain >>> some but not all of the water I'd have to copy the topology of my water >>> model and add the restraints, then rename (and group together) the atoms >>> I >>> want to freeze so that they're identified with the appropriate topology >>> file. Does this sound like it would work? Is there some other way that >>> you >>> might do it? >>> >>> Thanks >>> >>> On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall >>> wrote: >>> >>> Justin: I'll try using position restraints instead of freezing the water >>>> in the tube. Thanks for the tip. >>>> >>>> Bogdan: I don't think I'm using constraints other than freeze groups. I >>>> wasn't using energy group exclusions though. I tried running the >>>> >>> simulation >>> >>>> from the same initial configuration with newly-defined energy groups >>>> CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second >>>> for >>>> the free atoms. The list of exclusions reads: >>>> energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN >>>> >>>> Long story short, I'm roughly 15 ns into the simulation and the same two >>>> waters have jumped. I'll check the manual again though. Thanks. >>>> >>>> On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu >>> >>> gmail.com>wrote: >>> >>>> >>>> On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall >>>>> >>>> wrote: >>> >>>> Thanks Justin. I identified the offending waters using vmd (adding 1 >>>>>> >>>>> to >>> >>>> resID and atom number since vmd starts counting at 0) and checked >>>>>> confout.gro to make sure the coordinates matched up. I only have one >>>>>> >>>>> group >>>>> >>>>>> for all frozen atoms in the system, and these guys are definitely in >>>>>> >>>>> it. >>> >>>> >>>>> Are you using some kind of constraints ? Are you using energy group >>>>> exclusions to avoid interactions between frozen atoms ? If you search >>>>> the manual for "frozen" you'll find some warnings and recommendations. >>>>> >>>>> Cheers, >>>>> Bogdan >>>>> -- >>>>> gmx-users mailing listgmx-users at gromacs.org >>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>>>> posting! >>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to gmx-users-request at gromacs.org. >>>>> * Can't post? Read >>>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Alex Marshall >>>> M.Sc. Candidate >>>> Departm
Re: [gmx-users] Freeze group atoms changing position
Chris, is that for freeze groups or position restraints? On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > No need to rename... just make an .ndx group. > > -- original message -- > > As I understand it, position restraints for an atom are set in the topology > file and applied to that atom in each of that species. In order to restrain > some but not all of the water I'd have to copy the topology of my water > model and add the restraints, then rename (and group together) the atoms I > want to freeze so that they're identified with the appropriate topology > file. Does this sound like it would work? Is there some other way that you > might do it? > > Thanks > > On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall wrote: > > > Justin: I'll try using position restraints instead of freezing the water > > in the tube. Thanks for the tip. > > > > Bogdan: I don't think I'm using constraints other than freeze groups. I > > wasn't using energy group exclusions though. I tried running the > simulation > > from the same initial configuration with newly-defined energy groups > > CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for > > the free atoms. The list of exclusions reads: > > energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN > > > > Long story short, I'm roughly 15 ns into the simulation and the same two > > waters have jumped. I'll check the manual again though. Thanks. > > > > On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu gmail.com>wrote: > > > >> On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall > wrote: > >> > Thanks Justin. I identified the offending waters using vmd (adding 1 > to > >> > resID and atom number since vmd starts counting at 0) and checked > >> > confout.gro to make sure the coordinates matched up. I only have one > >> group > >> > for all frozen atoms in the system, and these guys are definitely in > it. > >> > >> Are you using some kind of constraints ? Are you using energy group > >> exclusions to avoid interactions between frozen atoms ? If you search > >> the manual for "frozen" you'll find some warnings and recommendations. > >> > >> Cheers, > >> Bogdan > >> -- > >> gmx-users mailing listgmx-users at gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-request at gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > > > > -- > > Alex Marshall > > M.Sc. Candidate > > Department of Applied Mathematics > > The University of Western Ontario > > > > > > > -- > Alex Marshall > M.Sc. > Department of Applied Mathematics > The University of Western Ontario > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freeze group atoms changing position
As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water model and add the restraints, then rename (and group together) the atoms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall wrote: > Justin: I'll try using position restraints instead of freezing the water > in the tube. Thanks for the tip. > > Bogdan: I don't think I'm using constraints other than freeze groups. I > wasn't using energy group exclusions though. I tried running the simulation > from the same initial configuration with newly-defined energy groups > CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for > the free atoms. The list of exclusions reads: > energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN > > Long story short, I'm roughly 15 ns into the simulation and the same two > waters have jumped. I'll check the manual again though. Thanks. > > On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu wrote: > >> On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall wrote: >> > Thanks Justin. I identified the offending waters using vmd (adding 1 to >> > resID and atom number since vmd starts counting at 0) and checked >> > confout.gro to make sure the coordinates matched up. I only have one >> group >> > for all frozen atoms in the system, and these guys are definitely in it. >> >> Are you using some kind of constraints ? Are you using energy group >> exclusions to avoid interactions between frozen atoms ? If you search >> the manual for "frozen" you'll find some warnings and recommendations. >> >> Cheers, >> Bogdan >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Alex Marshall > M.Sc. Candidate > Department of Applied Mathematics > The University of Western Ontario > > -- Alex Marshall M.Sc. Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freeze group atoms changing position
Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu wrote: > On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall wrote: > > Thanks Justin. I identified the offending waters using vmd (adding 1 to > > resID and atom number since vmd starts counting at 0) and checked > > confout.gro to make sure the coordinates matched up. I only have one > group > > for all frozen atoms in the system, and these guys are definitely in it. > > Are you using some kind of constraints ? Are you using energy group > exclusions to avoid interactions between frozen atoms ? If you search > the manual for "frozen" you'll find some warnings and recommendations. > > Cheers, > Bogdan > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freeze group atoms changing position
Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it. On Wed, Oct 24, 2012 at 9:22 PM, Justin Lemkul wrote: > > > On 10/24/12 3:17 PM, Alex Marshall wrote: > >> Hi all, >> >> I'm simulating a system of two reservoirs connected by a carbon nanotube. >> The reservoir wall atoms and carbon nanotube atoms are held in place using >> freeze groups at all times. I'm currently equilibrating the reservoirs >> separately by also freezing the water inside the nanotube, but after 20 ns >> two of the frozen water molecules have jumped outside of the nanotube into >> a supposedly inaccessible region. What could cause this? Should I be >> worried? >> >> > I would be. Frozen groups aren't supposed to move at all. Verify that > the problematic water molecules are indeed contained within whatever frozen > group(s) you have assigned in the .mdp file. Otherwise, there's no > immediate explanation, especially since other frozen atoms are staying > frozen. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Freeze group atoms changing position
Hi all, I'm simulating a system of two reservoirs connected by a carbon nanotube. The reservoir wall atoms and carbon nanotube atoms are held in place using freeze groups at all times. I'm currently equilibrating the reservoirs separately by also freezing the water inside the nanotube, but after 20 ns two of the frozen water molecules have jumped outside of the nanotube into a supposedly inaccessible region. What could cause this? Should I be worried? -- Thanks, Alex Marshall M.Sc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to create two parallel wall?
There's a built-in wall option. Check section 7.3.20 of the manual. Otherwise, you could just include coordinates and topologies for walls in your simulation. For your second question, g_density with appropriate index groups. On Wed, Sep 12, 2012 at 4:27 PM, Ali Alizadeh wrote: > Dear All users > > > How to create two parallel wall? > > How the component density profiles be measured between two walls? > > > Sincerely > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Measuring hydrogen bonding in a specific region
Thanks Justin, this is great.
On Tue, Jul 17, 2012 at 5:07 PM, Justin Lemkul wrote:
>
>
> On 7/17/12 4:57 PM, Andrew DeYoung wrote:
>>
>> Hi Justin,
>>
>> I am just curious, do you have experience writing such a shell script to
>> iterate over the index files (one per frame)? I am just curious, because
>> I
>> have been trying this, and I have found it very difficult to do using
>> bash.
>> Do you use a different shell language?
>>
>> Also, I wonder if anyone has ever posted such a shell script on this list.
>> When I look through the archives, I don't see one, but I could be wrong.
>>
>
> Assume we have 100 groups of arbitrary size and a fixed group (index group
> 0) in the index file to which we wish to calculate hydrogen bonds. Then
> assume we have 100 separate files (from trjconv -sep or whatever else)
> numbered sequentially, i.e. conf1.gro, conf2.gro...conf100.gro. A simple
> bash script that runs through the index groups corresponding to each of
> these coordinate files would be something like:
>
> #!/bin/bash
>
> for i in {1..100}
> do
> echo 0 $i | g_hbond -s topol.tpr -f conf$i.gro -n index.ndx
> done
>
>
> -Justin
>
> --
>
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Alex Marshall
M.Sc. Candidate
Department of Applied Mathematics
The University of Western Ontario
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Measuring hydrogen bonding in a specific region
Hi all, I have a system that consists of two distinct reservoirs filled with water+NaCl connected by a CNT. I want to measure the average number of hydrogen bonds per water in each reservoir as a function of time, but my current workflow for this is far too time-consuming to get any significant resolution: -Have trjconv dump frames to separate .gro files (for example, in 10ns increments) -use g_select to create a .ndx file with groups for the waters in either reservoir -run g_hbond on the .gro file with the appropriate .ndx file, record the number of hbonds and the number of donors for each reservoir Is there any way I could automate/improve this process? I have ten of these simulations longer than 100 ns to analyze, and I just need more data points than I can crank out manually. Thanks. -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Velocities in trjconv 4.5.5
I'm pretty sure .cpt files don't store velocity information. Try using a trr file instead. On Mon, Apr 23, 2012 at 4:40 AM, Ignacio Fernández Galván wrote: > Hi all, > > I'm trying to get a .gro file with velocities. This command line works in > 4.5.3: > > $ trjconv -f file.cpt -s file.tpr -o file.gro -pbc mol -center -boxcenter > zero -ur compact -ndec 6 > > But in 4.5.5 the output .gro file is written without the velocities, even > though the -vel option is listed as "yes" in the terminal. > > Has this been changed on purpose? Is there a way to get the old behaviour? > > If you wonder why I want this, I want to continue a simulation where the > coordinates of a frozen part of the system are slightly changed, so I need > a file with coordinates and velocities, and then modify the coordinates. > > Thanks, > Ignacio > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] can mdrun append output files without the proper .cpt?
Thanks Mark! On Tue, Jan 31, 2012 at 7:26 PM, Mark Abraham wrote: > On 28/01/2012 7:09 AM, Alex Marshall wrote: > > Hi all, > I was trying to extend my simulation but I used the wrong .tpr file when I > called mdrun_mpi. I didn't catch it in time and my checkpoint files were > overwritten. Now I've used GROMPP to extend the simulation (as directed in > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations), but > when I use mdrun_mpi -append with the extended .tpr file, new output files > are generated anyway. Is there a way around this, or will I just have to > use trjcat or something once the new run has finished? > > > The .cpt files contain checksums of the files that were written with them, > which are checked when attempting to append later. If they don't match, > mdrun is conservative and writes new files. So you will have to cut and > paste later. > > Mark > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] can mdrun append output files without the proper .cpt?
Hi all, I was trying to extend my simulation but I used the wrong .tpr file when I called mdrun_mpi. I didn't catch it in time and my checkpoint files were overwritten. Now I've used GROMPP to extend the simulation (as directed in http://www.gromacs.org/Documentation/How-tos/Extending_Simulations), but when I use mdrun_mpi -append with the extended .tpr file, new output files are generated anyway. Is there a way around this, or will I just have to use trjcat or something once the new run has finished? Thanks. -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Dimensionless units question
I'm trying to calculate the total electrostatic energy of the system, and the force in the Z direction on the particle placed above the lattice. It's a purely electrostatic problem, ideally LJ shouldn't come into it at all, but I don't know how else to convert the resulting energy and force to dimensionless units, which I must do because I was given reference values in dimensionless units. I guess I'm not actually using gmx.ff, I was just using the C6-C12 convention for LJ parameters used in that forcefield's ffnonbonded.itp. On Fri, Jul 29, 2011 at 3:50 PM, Amit Choubey wrote: > I am not sure what you want to measure. You mentioned that "force and > energy I calculate are still quite far from the reference values", now are > you only looking at electrostatic contributions to these or the total > contributions? If its total contribution then LJ parameters should also be > correct and for that you should switch to standard gromacs units. > > Also why do you need to use gmx.ff, seems to me that you already have the > parameters (ie the LJ parameters and charges) > > > On Fri, Jul 29, 2011 at 11:30 AM, Alex Marshall wrote: > >> Hi Amit, >> >> So if I understand you correctly, any LJ interaction I impose on these >> particles will be quite arbitrary because I'm only concerned with >> electrostatics, right? How then might I go about comparing the dimensionless >> reference values given with the values I calculated? I don't think I can >> simply compare their ratios, as there would still be a unit of length to >> deal with. >> >> Thanks, >> Alex >> >> On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey wrote: >> >>> Hi, >>> >>> reduced units works for LJ particles only. I am not sure if it works when >>> you include electrostatics. When you set charge = 1 it is 1electronic >>> charge. I would suggest not to use the reduced units for LJ in this >>> scenario. >>> >>> Amit >>> >>> On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall wrote: >>> >>>> Hi all, >>>> >>>> I'm trying to calculate the force on one particle and the total >>>> electrostatic energy of my system, which consists of a lattice of 25 evenly >>>> spaced charges in the xy plane and a single charge in the center above to >>>> preserve charge neutrality. The reference values I have been given are in >>>> dimensionless units, so I am tasked with either converting my output to >>>> dimensionless units or having gromacs work in reduced units from the get >>>> go. >>>> I have set the mass of each charge to 1, the magnitude of the charge on >>>> each >>>> particle to 1, and the values of the C6 and C12 parameters in my itp file >>>> to >>>> 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. >>>> I've turned off temperature coupling because this is purely a test of the >>>> handling of electrostatics with 3D Ewald summation plus the correction for >>>> slab geometry. However, the force and energy I calculate are still quite >>>> far >>>> from the reference values. Have I missed anything if I want my output to be >>>> in dimensionless units? >>>> >>>> Thanks, >>>> Alex >>>> >>>> -- >>>> gmx-users mailing listgmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/S
Re: [gmx-users] Dimensionless units question
Hi Amit, So if I understand you correctly, any LJ interaction I impose on these particles will be quite arbitrary because I'm only concerned with electrostatics, right? How then might I go about comparing the dimensionless reference values given with the values I calculated? I don't think I can simply compare their ratios, as there would still be a unit of length to deal with. Thanks, Alex On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey wrote: > Hi, > > reduced units works for LJ particles only. I am not sure if it works when > you include electrostatics. When you set charge = 1 it is 1electronic > charge. I would suggest not to use the reduced units for LJ in this > scenario. > > Amit > > On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall wrote: > >> Hi all, >> >> I'm trying to calculate the force on one particle and the total >> electrostatic energy of my system, which consists of a lattice of 25 evenly >> spaced charges in the xy plane and a single charge in the center above to >> preserve charge neutrality. The reference values I have been given are in >> dimensionless units, so I am tasked with either converting my output to >> dimensionless units or having gromacs work in reduced units from the get go. >> I have set the mass of each charge to 1, the magnitude of the charge on each >> particle to 1, and the values of the C6 and C12 parameters in my itp file to >> 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. >> I've turned off temperature coupling because this is purely a test of the >> handling of electrostatics with 3D Ewald summation plus the correction for >> slab geometry. However, the force and energy I calculate are still quite far >> from the reference values. Have I missed anything if I want my output to be >> in dimensionless units? >> >> Thanks, >> Alex >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Dimensionless units question
Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in dimensionless units, so I am tasked with either converting my output to dimensionless units or having gromacs work in reduced units from the get go. I have set the mass of each charge to 1, the magnitude of the charge on each particle to 1, and the values of the C6 and C12 parameters in my itp file to 4.0, since I'm just using gmx.ff for this (hopefully simple) calculation. I've turned off temperature coupling because this is purely a test of the handling of electrostatics with 3D Ewald summation plus the correction for slab geometry. However, the force and energy I calculate are still quite far from the reference values. Have I missed anything if I want my output to be in dimensionless units? Thanks, Alex -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Slab Ewald test
Hi all, I'm currently trying to run a simple test on how electrostatics are handled in gromacs when the slab Ewald summation is used. My system consists of 26 point charges, with 25 arranged in a square lattice in the XY plane and the 26th above the charge in the middle. My goal is to calculate the force on the particle above and the total electrostatic energy. I have written my own coordinate and topology files, and they grompp just fine, but when I try to mdrun for just one step, I get a segfault. Trajectory files are still produced, but when I try to have trjconv output the forces, it just writes the coordinates. The command I used was: trjconv -f traj.trr -s topol.tpr -n index.ndx -novel -force -o results.gro I've set nxtxout, nxtvout and nxtfout to 1 in my mdp file, so if not for the segfault, I believe I should have force data. How can I fix the segfault? .itp file for charges: [ moleculetype ] ; Name nrexcl CHR 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 H 1 CHR H3 1 1 1 H 0 0 ; qtot 0 2 H 1 CHR H6 2 -1 1 H 0 0 ; qtot 0 3 H 2 CHR H3 3 1 1 H 0 0 ; qtot 0 4 H 2 CHR H6 4 -1 1 H 0 0 ; qtot 0 5 H 3 CHR H3 5 1 1 H 0 0 ; qtot 0 6 H 3 CHR H6 6 -1 1 H 0 0 ; qtot 0 7 H 4 CHR H3 7 1 1 H 0 0 ; qtot 0 8 H 4 CHR H6 8 -1 1 H 0 0 ; qtot 0 9 H 5 CHR H3 9 1 1 H 0 0 ; qtot 0 10 H 5 CHR H6 10 -1 1 H 0 0 ; qtot 0 11 H 6 CHR H3 11 1 1 H 0 0 ; qtot 0 12 H 6 CHR H6 12 -1 1 H 0 0 ; qtot 0 13 H 7 CHR H3 13 1 1 H 0 0 ; qtot 0 14 H 7 CHR H6 14 -1 1 H 0 0 ; qtot 0 15 H 8 CHR H3 15 1 1 H 0 0 ; qtot 0 16 H 8 CHR H6 16 -1 1 H 0 0 ; qtot 0 17 H 9 CHR H3 17 1 1 H 0 0 ; qtot 0 18 H 9 CHR H6 18 -1 1 H 0 0 ; qtot 0 19 H 10 CHR H3 19 1 1 H 0 0 ; qtot 0 20 H 10 CHR H6 20 -1 1 H 0 0 ; qtot 0 21 H 11 CHR H3 21 1 1 H 0 0 ; qtot 0 22 H 11 CHR H6 22 -1 1 H 0 0 ; qtot 0 23 H 12 CHR H3 23 1 1 H 0 0 ; qtot 0 24 H 12 CHR H6 24 -1 1 H 0 0 ; qtot 0 25 H 13 CHR H3 25 1 1 H 0 0 ; qtot 0 26 H 13 CHR H6 26 -1 1 H 0 0 ; qtot 0 Thanks, Alex Marshall -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
