[gmx-users] gmx chi: chi.log output all rotamers always 0
hi list, using gmx chi -s file.tpr -f file.xtc -maxchi 1 -all -g -o i try to get the different rotamers and transition between them per ns. however, the chi.log output file has for every residue only this: Residue LYS12 Angle [ AI, AJ, AK, AL] rotamers 0 g(-) t g(+) Chi1[ 120, 122, 124, 127]0.000.000.000.00 any idea why? the xtc file is aligned and pbc was solved beforehand. Thank you very much, Max -- 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] Verify if position restrain was applied
Dear list, I wanted to know if there is a way to verify if the position restrain was applied correctly to the atoms in question. Couldn’t find anything in the log file. Thank you, 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] Verify if position restrain was applied
I saw that you can use gmx energy to select Position-Rest. and Constr.-rmsd but I was looking for the atom id on which the position restrains acted. Looking at my trajectory I am not sure if I did the correct configuration since my energy from gmx energy -> Position-Rest shows a maximum of 20kJ/mol but my molecule moved around its position with a restrain of 1000 1000 1000. Max > On Oct 26, 2015, at 4:02 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > > On 26/10/15 20:58, Ebert Maximilian wrote: >> Dear list, >> >> I wanted to know if there is a way to verify if the position restrain was >> applied correctly to the atoms in question. Couldn’t find anything in the >> log file. >> > How about position restraint energy? > >> Thank you, >> >> > > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > 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] Verify if position restrain was applied
Thanks I didn’t know the dump command. Good evening On Oct 26, 2015, at 4:50 PM, Justin Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: On 10/26/15 4:44 PM, Ebert Maximilian wrote: Thank you for your clarification that makes sense now in my simulation. Never the less is there an output per atom somewhere? Everything is in the .tpr file. Use gmx dump and redirect to a file and look through. -Justin Thank you very much On Oct 26, 2015, at 4:37 PM, David van der Spoel <sp...@xray.bmc.uu.se<mailto:sp...@xray.bmc.uu.se>> wrote: On 26/10/15 21:06, Ebert Maximilian wrote: I saw that you can use gmx energy to select Position-Rest. and Constr.-rmsd but I was looking for the atom id on which the position restrains acted. Looking at my trajectory I am not sure if I did the correct configuration since my energy from gmx energy -> Position-Rest shows a maximum of 20kJ/mol but my molecule moved around its position with a restrain of 1000 1000 1000. Max On Oct 26, 2015, at 4:02 PM, David van der Spoel <sp...@xray.bmc.uu.se<mailto:sp...@xray.bmc.uu.se>> wrote: On 26/10/15 20:58, Ebert Maximilian wrote: Dear list, I wanted to know if there is a way to verify if the position restrain was applied correctly to the atoms in question. Couldn’t find anything in the log file. restraint mean 1000 kJ/mol/nm^2, so 20 kJ/mol means 0.02 nm^2, or 0.14 nm for 1 atom. How about position restraint energy? Thank you, mailto:sp...@xray.bmc.uu.se>http://folding.bmc.uu.se -- 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<mailto:gmx-users-requ...@gromacs.org>. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se<mailto:sp...@xray.bmc.uu.se>http://folding.bmc.uu.se -- 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<mailto:gmx-users-requ...@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 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu<mailto:jalem...@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-requ...@gromacs.org<mailto: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] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?
Thanks for the answer. I was checking the CHARMM22 All-Hydrogen Parameter File for Proteins par_all22_prot.inp and the section non-bonded: nitrogens N 0.00 -0.20 1.85 0.00 -0.000100 1.85 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC20.00 -0.20 1.85 ! ALLOW POL ! JG 8/27/89; note: NH1 in ARG was changed to NC2. NH10.00 -0.20 1.85 0.00 -0.20 1.55 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH20.00 -0.20 1.85 ! ALLOW POL ! adm jr. NH30.00 -0.20 1.85 ! ALLOW POL ! adm jr. NP 0.00 -0.20 1.85 ! ALLOW PRO ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 NPH0.00 -0.20 1.85 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR10.00 -0.20 1.85 ! ALLOW ARO ! His, adm jr., 9/4/89 NR20.00 -0.20 1.85 ! ALLOW ARO ! His, adm jr., 9/4/89 NR30.00 -0.20 1.85 ! ALLOW ARO ! His, adm jr., 9/4/89 NY 0.00 -0.20 1.85 ! ALLOW ARO ! trp, JWK All nitrogen have the same LJ parameter. I haven’t checked CGenFF but I will definitely look into that. Thanks for you comment. Max > On Oct 22, 2015, at 12:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 10/22/15 11:04 AM, Ebert Maximilian wrote: >> Dear list, >> >> I already asked the question in the AMBER list but couldn’t get an answer. >> So I try my luck here even though it is a bit off topic in the GROMACS list. >> I was wondering why the different atom types of H, C and O have different >> LJ-parameter but for all the different types of N we see the identical >> parameters in OPLS, AMBER and CHARMM? >> > > Sometimes that's just the way force fields work out. Electrostatics are > tuned first, and then condensed phase interactions are targeted for LJ > refinement. Given the nature of most N interactions (either lone pair or via > polar/hydrogen bonding interactions with an H), the electrostatics generally > dominate, so a generic LJ parameter that is common to different moieties is > sufficient. > > In CGenFF, there are several N types with different LJ, though the > biomolecular parts of the CHARMM force field share the same parameters. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@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-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] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?
Dear list, I already asked the question in the AMBER list but couldn’t get an answer. So I try my luck here even though it is a bit off topic in the GROMACS list. I was wondering why the different atom types of H, C and O have different LJ-parameter but for all the different types of N we see the identical parameters in OPLS, AMBER and CHARMM? Thank you very much, Max -- 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] GMXLIB does not induce residuetype.dat
Hi,
sorry for responding that late. The problem in the end was that first in
specbonds the search length was 0.1nm off so it appeared for this structure as
if the file wasn’t used but it was. and second i had the merge the PDB chain
since there was a TER between the hetero atom and the protein residues.
so now all is good. putting in ~/.bash_profile
GMXLIB=
works fine. Thanks for your help,
Max
> On Oct 3, 2015, at 1:03 PM, João M. Damas <jmda...@itqb.unl.pt> wrote:
>
> The definition seems fine. In the pdb2gmx standard output, you should check
> that directory is the one being opened.
>
> If it is, please do a "ls ${GMXLIB}" and check the output, if the file is
> there (and not inside the ff directory). Even though I am guessing this is
> just a typo problem, and you are using "residuestype.dat" while the file is
> "residuetypes.dat".
>
> João
>
> On Sat, Oct 3, 2015 at 4:55 AM, Barnett, James W <jbarn...@tulane.edu>
> wrote:
>
>> On Thu, 2015-10-01 at 20:21 +, Ebert Maximilian wrote:
>>> Dear list,
>>>
>>> I have my own force field working folder so I cloned the entire top
>> folder to
>>> no mess with the original files. I added residues to the residue type
>> file to
>>> add my residues to the protein group. My FF is included due to the GMXLIB
>>> environmental variable but my modified residuestype.dat not. Any idea
>> why?
>>
>> Can you give an example of how it is not included? Is there a specific
>> GROMACS
>> command that is not finding it, or is it something else?
>>
>> --
>> James “Wes” Barnett, Ph.D. Candidate
>> Louisiana Board of Regents Fellow
>>
>> Chemical and Biomolecular Engineering
>> Tulane University
>> 341-B Lindy Boggs Center for Energy and Biotechnology
>> 6823 St. Charles Ave
>> New Orleans, Louisiana 70118-5674
>> jbarn...@tulane.edu
>> --
>> 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.
>>
>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
> --
> 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!
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Re: [gmx-users] RMSF calculation of carbon alpha
Like gmx rms the gmx rmsf tool should be extended to align and calculate on different index groups. That would be helpful. Also maybe we could add some information about the -res flag and the behaviour for aligning and calculating the the gmx rmsf help text. How could I suggest that officially? Max > On Oct 6, 2015, at 2:36 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > Right :) > > Cheers, > > Tsjerk > > On Mon, Oct 5, 2015 at 11:07 PM, Ebert Maximilian <m.eb...@umontreal.ca> > wrote: > >> Thanks for the clarification Tsjerk. So my previous assumption was right. >> Basically if I want to align on the backbone but want the RMSF of Calpha I >> need to align first, save the trajectory and do RMSF with -nofit right? >> >> Max >> >>> On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >>> >>> Hi Ebert, >>> >>> Use C-alpha as the group. Yes, it will be used for fitting and >> calculation >>> of the RMSF. >>> >>> Cheers, >>> >>> Tsjerk >>> On Oct 5, 2015 22:44, "Ebert Maximilian" <m.eb...@umontreal.ca> wrote: >>> >>>> Oh infact no thats not the case it is still the RMSF of all atoms in the >>>> residue. So back to my initial question. How can I calculate the RMSF on >>>> the Ca of each residue? >>>> >>>> Sorry if this caused any confusion. >>>> >>>> Max >>>> >>>>> On Oct 5, 2015, at 4:36 PM, Ebert Maximilian <m.eb...@umontreal.ca> >>>> wrote: >>>>> >>>>> I think I can answer my own question again. The group you use for root >>>> mean square calculation is also the RMSF group. If the group has more >> than >>>> one atom per residue and I use -res I get the average RMSF of all atoms >> per >>>> residue. >>>>> >>>>> Hope this is correct. >>>>> >>>>> Max >>>>> >>>>>> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian <m.eb...@umontreal.ca> >>>> wrote: >>>>>> >>>>>> Hi there, >>>>>> >>>>>> I want to calculate ht RMSF of the carbon alpha. First which atoms are >>>> used if I calculate the RMSF per residue with -res and how can I >> calculate >>>> the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input >>>> except for the group of the alignment for the -fit >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Max >>>>>> -- >>>>>> 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
[gmx-users] RMSF calculation of carbon alpha
Hi there, I want to calculate ht RMSF of the carbon alpha. First which atoms are used if I calculate the RMSF per residue with -res and how can I calculate the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except for the group of the alignment for the -fit Thank you, Max -- 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] RMSF calculation of carbon alpha
Oh infact no thats not the case it is still the RMSF of all atoms in the residue. So back to my initial question. How can I calculate the RMSF on the Ca of each residue? Sorry if this caused any confusion. Max > On Oct 5, 2015, at 4:36 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > > I think I can answer my own question again. The group you use for root mean > square calculation is also the RMSF group. If the group has more than one > atom per residue and I use -res I get the average RMSF of all atoms per > residue. > > Hope this is correct. > > Max > >> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: >> >> Hi there, >> >> I want to calculate ht RMSF of the carbon alpha. First which atoms are used >> if I calculate the RMSF per residue with -res and how can I calculate the >> RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except >> for the group of the alignment for the -fit >> >> Thank you, >> >> Max >> -- >> 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] RMSF calculation of carbon alpha
Thanks for the clarification Tsjerk. So my previous assumption was right. Basically if I want to align on the backbone but want the RMSF of Calpha I need to align first, save the trajectory and do RMSF with -nofit right? Max > On Oct 5, 2015, at 4:54 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > Hi Ebert, > > Use C-alpha as the group. Yes, it will be used for fitting and calculation > of the RMSF. > > Cheers, > > Tsjerk > On Oct 5, 2015 22:44, "Ebert Maximilian" <m.eb...@umontreal.ca> wrote: > >> Oh infact no thats not the case it is still the RMSF of all atoms in the >> residue. So back to my initial question. How can I calculate the RMSF on >> the Ca of each residue? >> >> Sorry if this caused any confusion. >> >> Max >> >>> On Oct 5, 2015, at 4:36 PM, Ebert Maximilian <m.eb...@umontreal.ca> >> wrote: >>> >>> I think I can answer my own question again. The group you use for root >> mean square calculation is also the RMSF group. If the group has more than >> one atom per residue and I use -res I get the average RMSF of all atoms per >> residue. >>> >>> Hope this is correct. >>> >>> Max >>> >>>> On Oct 5, 2015, at 2:46 PM, Ebert Maximilian <m.eb...@umontreal.ca> >> wrote: >>>> >>>> Hi there, >>>> >>>> I want to calculate ht RMSF of the carbon alpha. First which atoms are >> used if I calculate the RMSF per residue with -res and how can I calculate >> the RMSF of carbon alpha or NH vector etc? Can’t seem to find an input >> except for the group of the alignment for the -fit >>>> >>>> Thank you, >>>> >>>> Max >>>> -- >>>> 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] RMSF calculation of carbon alpha
I think I can answer my own question again. The group you use for root mean square calculation is also the RMSF group. If the group has more than one atom per residue and I use -res I get the average RMSF of all atoms per residue. Hope this is correct. Max > On Oct 5, 2015, at 2:46 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > > Hi there, > > I want to calculate ht RMSF of the carbon alpha. First which atoms are used > if I calculate the RMSF per residue with -res and how can I calculate the > RMSF of carbon alpha or NH vector etc? Can’t seem to find an input except for > the group of the alignment for the -fit > > Thank you, > > Max > -- > 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] GMXLIB does not induce residuetype.dat
thanks for the answer. in the console i wrote: GMXLIB="~/GROMACS/gromacs_ff/“ export GMXLIB the shell is GNU bash, version 4.1.2(1)-release Max > On Oct 2, 2015, at 9:22 AM, João M. Damas <jmda...@itqb.unl.pt> wrote: > > How are you defining the GMXLIB variable in your script? Please give us > some more information (inputs and outputs) for us to be able to help you. > > João > > On Thu, Oct 1, 2015 at 9:21 PM, Ebert Maximilian <m.eb...@umontreal.ca> > wrote: > >> Dear list, >> >> I have my own force field working folder so I cloned the entire top folder >> to no mess with the original files. I added residues to the residue type >> file to add my residues to the protein group. My FF is included due to the >> GMXLIB environmental variable but my modified residuestype.dat not. Any >> idea why? >> >> 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. >> > > > > -- > João M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 > -- > 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] Free oxygen in water AMBER FF definition to use in GROMACS
I found a definition for oxygen in the paper: Effective Simulations of Gas Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O2 Pathways and Escape Routes in T-state Deoxyhemoglobin they use CHARMM as FF and I will use AMBER99SB-ILDN so not ideal because it was not calculate with the same FF in mind but for such a simple molecule it should be fine. have a good weekend, max > On Sep 24, 2015, at 5:59 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > > Hi there, > > I wanted to know if anyone has AMBER FF definition of oxygen, which I could > use to simulate oxygen in water. > > Thank you very much, > > Max > > -- > 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] Possibility to keep molecules during MD at a certain distance
Hi list, I am trying to enforce a minimum pair distance of certain molecules in my MD using a network of repulsive half-harmonic distance-restraining potentials with a specific force constant. How would I do that? Is it the [ bonds ] type 6 option? If so do I have to write a bond for each molecule with each molecule? Thanks for the help -- 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] GMXLIB does not induce residuetype.dat
Dear list, I have my own force field working folder so I cloned the entire top folder to no mess with the original files. I added residues to the residue type file to add my residues to the protein group. My FF is included due to the GMXLIB environmental variable but my modified residuestype.dat not. Any idea why? 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.
Re: [gmx-users] GROMACS with AMBER heme parameters
Yeah that is what I thought but that’s life. One more question.In the [ atomtypes ] section I need the sigma and epsilon value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is in nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in angstroem and defined as r0 which is sigma *( the 6th root of 2). So I picked an atomtype which is defined in the same way in AMBER and GAFF to see if I am doing the conversion right. A standard carbon CA is similar in both since the definition is taken from OPLS: GAFF ca r0: 1.9080 epsilon: 0.0860 If I look in the AMBER FF in GROMACS this changes to AMBER FF in GROMACS CA sigma: 3.39967e-01 epsilon: 3.59824e-01 If I convert now the 0.086 kcal/mol into kj/mol I get 3.59824e-01 which is as expected. However, for sigma I get only 1.6998e-01 instead of 3.39967e-01, which is half. Why is the sigma value in GROMACS two times the sigma value in GAFF? Is GAFF using Rmin/2 and GROMACS Rmin? It seems like it but I just wanted to be sure. Thanks > On Sep 25, 2015, at 4:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 9/25/15 4:40 PM, Ebert Maximilian wrote: >> I read that and this is the way I added the cysteine to AMBER which connects >> to the heme. Now I am adding the heme but the FF definition for bonds, >> angles, etc are all in lower case for the GAFF FF. From you answer I guess I >> need to add these lower case atom types and the bonds, angles, etc >> definition from the GAFF FF to the AMBER FF manually. >> > > Indeed, which is what steps 3 and 4 tell you. Adding a residue is simple, > but if that residue involves modifications to the force field, then there is > more work to be done. > > -Justin > >> Not much fun but I will share the work here in the end. Maybe this will help >> people who want to simulate heme containing proteins in GROMACS and >> AMBER99SB-ILDN. >> >> Have a good weekend, >> Max >> >> >> On Sep 25, 2015, at 4:25 PM, Justin Lemkul >> <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: >> >> >> >> On 9/25/15 4:22 PM, Ebert Maximilian wrote: >> Since the heme definition in AMBER uses GAFF atom types how do I get the >> GAFF FF to work in GROMACS? I would need all the bonded and non bonded >> definitions of GAFF for the heme in der AMBER FF port in GROMACS right? >> >> >> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field >> >> -Justin >> >> Max >> >> On Sep 25, 2015, at 1:36 PM, Justin Lemkul >> <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: >> >> >> >> On 9/25/15 1:32 PM, Ebert Maximilian wrote: >> Hi there, >> >> I am trying to simulate a heme containing protein. I found AMBER heme >> parameters in the mol2 and frcmod file format. I know that I can generate >> .itp files containing the parameters, which I can later add to my .top file. >> However, it would be much easier to use pdb2gmx directly without stripping >> the heme and the cysteine binding the heme and later manually add it again. I >> added the cysteine to the standard amber force field. However, before adding >> the heme manually I wanted to know if there is a way to load an itp file >> while executing pdb2gmx? >> >> >> pdb2gmx does not need .itp information. grompp does. Add the parameters to >> ffbonded.itp or ffnonbonded.itp as needed. >> >> How would you add the information from the cysteine in mol2 format and the >> heme in mol2/frcmod format to amber in gromacs? >> >> >> Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys >> is already supported via specbond.dat. >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu<mailto:jalem...@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 >> >>
Re: [gmx-users] GROMACS with AMBER heme parameters
I will answer my own question: I found in another post that indeed in GROMACS its Rmin. Thanks > On Sep 25, 2015, at 5:25 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > > Yeah that is what I thought but that’s life. > > One more question.In the [ atomtypes ] section I need the sigma and epsilon > value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is > in nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in > angstroem and defined as r0 which is sigma *( the 6th root of 2). > > So I picked an atomtype which is defined in the same way in AMBER and GAFF to > see if I am doing the conversion right. A standard carbon CA is similar in > both since the definition is taken from OPLS: > > GAFF ca r0: 1.9080 epsilon: 0.0860 > > If I look in the AMBER FF in GROMACS this changes to > > AMBER FF in GROMACS CA sigma: 3.39967e-01 epsilon: 3.59824e-01 > > If I convert now the 0.086 kcal/mol into kj/mol I get 3.59824e-01 which is as > expected. However, for sigma I get only 1.6998e-01 instead of 3.39967e-01, > which is half. Why is the sigma value in GROMACS two times the sigma value in > GAFF? Is GAFF using Rmin/2 and GROMACS Rmin? It seems like it but I just > wanted to be sure. > > Thanks > >> On Sep 25, 2015, at 4:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >> >> On 9/25/15 4:40 PM, Ebert Maximilian wrote: >>> I read that and this is the way I added the cysteine to AMBER which >>> connects to the heme. Now I am adding the heme but the FF definition for >>> bonds, angles, etc are all in lower case for the GAFF FF. From you answer I >>> guess I need to add these lower case atom types and the bonds, angles, etc >>> definition from the GAFF FF to the AMBER FF manually. >>> >> >> Indeed, which is what steps 3 and 4 tell you. Adding a residue is simple, >> but if that residue involves modifications to the force field, then there is >> more work to be done. >> >> -Justin >> >>> Not much fun but I will share the work here in the end. Maybe this will >>> help people who want to simulate heme containing proteins in GROMACS and >>> AMBER99SB-ILDN. >>> >>> Have a good weekend, >>> Max >>> >>> >>> On Sep 25, 2015, at 4:25 PM, Justin Lemkul >>> <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: >>> >>> >>> >>> On 9/25/15 4:22 PM, Ebert Maximilian wrote: >>> Since the heme definition in AMBER uses GAFF atom types how do I get the >>> GAFF FF to work in GROMACS? I would need all the bonded and non bonded >>> definitions of GAFF for the heme in der AMBER FF port in GROMACS right? >>> >>> >>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field >>> >>> -Justin >>> >>> Max >>> >>> On Sep 25, 2015, at 1:36 PM, Justin Lemkul >>> <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: >>> >>> >>> >>> On 9/25/15 1:32 PM, Ebert Maximilian wrote: >>> Hi there, >>> >>> I am trying to simulate a heme containing protein. I found AMBER heme >>> parameters in the mol2 and frcmod file format. I know that I can generate >>> .itp files containing the parameters, which I can later add to my .top file. >>> However, it would be much easier to use pdb2gmx directly without stripping >>> the heme and the cysteine binding the heme and later manually add it again. >>> I >>> added the cysteine to the standard amber force field. However, before adding >>> the heme manually I wanted to know if there is a way to load an itp file >>> while executing pdb2gmx? >>> >>> >>> pdb2gmx does not need .itp information. grompp does. Add the parameters >>> to ffbonded.itp or ffnonbonded.itp as needed. >>> >>> How would you add the information from the cysteine in mol2 format and the >>> heme in mol2/frcmod format to amber in gromacs? >>> >>> >>> Charges and connectivity go in the .rtp entry. Heme ligation by His and >>> Cys is already supported via specbond.dat. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Heal
Re: [gmx-users] GROMACS with AMBER heme parameters
Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF FF to work in GROMACS? I would need all the bonded and non bonded definitions of GAFF for the heme in der AMBER FF port in GROMACS right? Max > On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 9/25/15 1:32 PM, Ebert Maximilian wrote: >> Hi there, >> >> I am trying to simulate a heme containing protein. I found AMBER heme >> parameters in the mol2 and frcmod file format. I know that I can generate >> .itp files containing the parameters, which I can later add to my .top file. >> However, it would be much easier to use pdb2gmx directly without stripping >> the heme and the cysteine binding the heme and later manually add it again. I >> added the cysteine to the standard amber force field. However, before adding >> the heme manually I wanted to know if there is a way to load an itp file >> while executing pdb2gmx? >> > > pdb2gmx does not need .itp information. grompp does. Add the parameters to > ffbonded.itp or ffnonbonded.itp as needed. > >> How would you add the information from the cysteine in mol2 format and the >> heme in mol2/frcmod format to amber in gromacs? >> > > Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys > is already supported via specbond.dat. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@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-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] GROMACS with AMBER heme parameters
I read that and this is the way I added the cysteine to AMBER which connects to the heme. Now I am adding the heme but the FF definition for bonds, angles, etc are all in lower case for the GAFF FF. From you answer I guess I need to add these lower case atom types and the bonds, angles, etc definition from the GAFF FF to the AMBER FF manually. Not much fun but I will share the work here in the end. Maybe this will help people who want to simulate heme containing proteins in GROMACS and AMBER99SB-ILDN. Have a good weekend, Max On Sep 25, 2015, at 4:25 PM, Justin Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: On 9/25/15 4:22 PM, Ebert Maximilian wrote: Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF FF to work in GROMACS? I would need all the bonded and non bonded definitions of GAFF for the heme in der AMBER FF port in GROMACS right? http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin Max On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: On 9/25/15 1:32 PM, Ebert Maximilian wrote: Hi there, I am trying to simulate a heme containing protein. I found AMBER heme parameters in the mol2 and frcmod file format. I know that I can generate .itp files containing the parameters, which I can later add to my .top file. However, it would be much easier to use pdb2gmx directly without stripping the heme and the cysteine binding the heme and later manually add it again. I added the cysteine to the standard amber force field. However, before adding the heme manually I wanted to know if there is a way to load an itp file while executing pdb2gmx? pdb2gmx does not need .itp information. grompp does. Add the parameters to ffbonded.itp or ffnonbonded.itp as needed. How would you add the information from the cysteine in mol2 format and the heme in mol2/frcmod format to amber in gromacs? Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys is already supported via specbond.dat. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu<mailto:jalem...@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-requ...@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 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu<mailto:jalem...@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-requ...@gromacs.org<mailto: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] GROMACS with AMBER heme parameters
Hi there, I am trying to simulate a heme containing protein. I found AMBER heme parameters in the mol2 and frcmod file format. I know that I can generate .itp files containing the parameters, which I can later add to my .top file. However, it would be much easier to use pdb2gmx directly without stripping the heme and the cysteine binding the heme and later manually add it again. I added the cysteine to the standard amber force field. However, before adding the heme manually I wanted to know if there is a way to load an itp file while executing pdb2gmx? How would you add the information from the cysteine in mol2 format and the heme in mol2/frcmod format to amber in gromacs? Thank you very much, Max -- 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] Free oxygen in water AMBER FF definition to use in GROMACS
Hi there, I wanted to know if anyone has AMBER FF definition of oxygen, which I could use to simulate oxygen in water. Thank you very much, Max -- 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] Load GROMACS trajectory with atom types and water in VMD
Dear list, I am not sure if this is a question for the VMD or GROMACS mailing list. However, I try to load a trr/xtc trajectory into VMD and want to keep the atom types. Since top and tpr files are not an input for VMD the atom type and name is the same as the structure file is PDB or GRO. I also tried top2psf but I guess since I have water and need the water in the trajectory I can’t use the script. Any idea how I could load the atom types? Thank you very much. Max -- 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] Load GROMACS trajectory with atom types and water in VMD
Hi, for the implicit ligand sampling module in VMD you need a loaded trajectory with the correct atom types. i guess I have to load them manually from another file into VMD. Max > On Sep 24, 2015, at 4:43 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > You can get what is in the structure file, and that is all. Since the atom > name is not the name of the force-field atom type, I don't think you can do > what you want. It is likely that whatever you were planning to do with atom > types you can do with the VMD selection syntax. > > Mark > > On Thu, Sep 24, 2015 at 10:28 PM Ebert Maximilian <m.eb...@umontreal.ca> > wrote: > >> Dear list, >> >> I am not sure if this is a question for the VMD or GROMACS mailing list. >> However, I try to load a trr/xtc trajectory into VMD and want to keep the >> atom types. Since top and tpr files are not an input for VMD the atom type >> and name is the same as the structure file is PDB or GRO. I also tried >> top2psf but I guess since I have water and need the water in the trajectory >> I can’t use the script. Any idea how I could load the atom types? >> >> Thank you very much. >> >> Max >> >> -- >> 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] Creating a box of water with density 1000 g/l
Hi there, I am wondering if there is a better way to create a box with water of a certain size than: gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512 To get a density of roughly 1000 g/l i would need to add 512 molecules in such a box. But the script only adds 502. I could play with the scale parameter but sometimes I have problems during minimization with messages like: Water molecule starting at atom 1465 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Thank you very much, Max -- 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] Creating a box of water with density 1000 g/l
The reason is that I try to reproduce the experiment from the paper System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions. before calculating the self diffusion coefficient for my organic solvent i wanted to see if my system setup is correct. the authors used 33 water molecules per nm^3. Therefore, I try to create a box in GROMACS with L=2.494 and fit 512 molecules of TIP3P water in. The reason the authors used these 33 molecules is to get about 1bar during the NVT without barostat. Max > On Sep 10, 2015, at 4:56 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 9/10/15 4:44 PM, Ebert Maximilian wrote: >> Hi there, >> >> I am wondering if there is a better way to create a box with water of a >> certain size than: >> >> gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512 >> >> To get a density of roughly 1000 g/l i would need to add 512 molecules in >> such a box. But the script only adds 502. I could play with the scale >> parameter but sometimes I have problems during minimization with messages >> like: >> >> Water molecule starting at atom 1465 can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> > > The density will anyway be dictated by the water model itself; none of the > common ones achieve exactly 1000 g/L. In principle, you could expand the box > very slightly, then re-size the box and simulate with NVT (thus constant > density), but at that point you're really manipulating the outcome, and I > don't know why you would need to go to such lengths. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@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-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] OPLS/AA parameters for 2-propanol
Thanks for the answer again. So I saw that for self-diffusion and viscosity I can just use gmx tcaf and gmx msd. As an experimental setup, would a squared box with 500 molecules of 2-propanol in NPT equilibration for a 10ns be a good system to use tcaf and msd? For the heat of vaporization I saw that I could calculate DHvap = - + RT is just Epot of the same MD I described above but for I need a new calculation. If I understood it correctly I would need a box with the same number of molecules as in the previous calculation but separate them with a lot of space (50nm was suggested). In addition, turn off PBC, PME, L-J and coulomb cut-offs. Get Epot from this calculation and use the formular. Would these approaches be correct? Thank you very much. Max > On Sep 2, 2015, at 5:02 PM, Vitaly V. Chaban <vvcha...@gmail.com> wrote: > > It is difficult to get a very wrong density, especially for relatively > rigid compounds. In the meantime, deviations of density within 2% of > the experimental value should be admitted acceptable. > > A better criterion is to compare self-diffusion or viscosity to the > experiment. Another famous property for parametrization is heat of > vaporization. > > > > > > > On Wed, Sep 2, 2015 at 3:22 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: >> Thanks for the reply. I think I found relatively good atom types for iso >> propanol and derived the partial charges using antechamber and red server. I >> next check the density of pure iso propanol and used the closest definition >> to the real value. Iso propanol is used as co-solvent with water with a >> water:iso propanol ration of 90:10. I will just use my derived parameters >> then. >> >> Thanks for your replies. >> >> Max >> >>> On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban <vvcha...@gmail.com> wrote: >>> >>> Normally, this sort of things is done via mechanical combining of the >>> known groups -- CH3, -CH, OH -- from the force field. >>> >>> If your goal is to increase accuracy for pure 2-propanol per se, then >>> play with the distribution of electronic density between OH and CH. >>> >>> If 2-propanol is to be used as a solvent for somwthing else, this does >>> ultimately not pay off. >>> >>> >>> >>> >>> >>> >>> >>> >>>> On Wed, Sep 2, 2015 at 11:42 AM, Ebert Maximilian <m.eb...@umontreal.ca> >>>> wrote: >>>> I saw the papers you mentioned but one is a not clear how they >>>> parameterized, one is missing the supporting material and the last is not >>>> showing the parameters they used. I will check with the initial paper of >>>> Jorgensen again but if I recall it correctly he mentioned some problems >>>> with iso-propanol. >>>> >>>> strange that such a common organic solvent is not easily accessible for >>>> OPLS. >>>> >>>> thanks for your help johnny! >>>> >>>> Max >>>> >>>>> On Sep 1, 2015, at 11:41 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: >>>>> >>>>> that was by google. I haven't parametrized forcefields. >>>>> did they just put the pieces in >>>>> http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work >>>>> for 2-propanol? >>>>> >>>>> >>>>>> On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu <johnny.lu...@gmail.com> >>>>>> wrote: >>>>>> >>>>>> Not sure if those are for 2-propanol as a liquid or interaction between >>>>>> 2-propanol and protein. >>>>>> from googling "2 propanol opls/aa" >>>>>> >>>>>> 1. Development and Testing of the OPLS All-Atom Force Field on >>>>>> Conformational Energetics and Properties of Organic Liquids >>>>>>The parameters are in the supporting info. >>>>>>Seems not exactly 2-propanol. But it has parameter for organic >>>>>> liquids. >>>>>>"OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols" >>>>>>http://pubs.acs.org/doi/abs/10.1021/ja9621760 >>>>>> >>>>>> 2. A statistical model of hydrogen bond networks in liquid alcohols >>>>>> >>>>>> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf >>>>>> >>>>>&
Re: [gmx-users] OPLS/AA parameters for 2-propanol
Hi justin, thank you for the answer. From your experience to calculate the shear viscosity with gmx tcaf for the correction term your mentioned (2.837297kBT/(6πηL)) would a trajectory with coordinates and velocities every 1 ps enough? Thanks On Sep 2, 2015, at 9:55 PM, Justin Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: On 9/2/15 9:47 PM, Ebert Maximilian wrote: Thanks for the answer again. So I saw that for self-diffusion and viscosity I can just use gmx tcaf and gmx msd. As an experimental setup, would a squared box with 500 molecules of 2-propanol in NPT equilibration for a 10ns be a good system to use tcaf and msd? Remember to correct for finite size effects in the diffusion constant (dx.doi.org/10.1021/jp0477147<http://dx.doi.org/10.1021/jp0477147>) For the heat of vaporization I saw that I could calculate DHvap = - + RT is just Epot of the same MD I described above but for I need a new calculation. If I understood it correctly I would need a box with the same number of molecules as in the previous calculation but separate them with a lot of space (50nm was suggested). In addition, turn off PBC, PME, L-J and coulomb cut-offs. Get Epot from this calculation and use the formular. More simply, divide by the number of molecules and just simulate one molecule in the gas phase (infinite cutoffs, no PBC) for . -Justin Would these approaches be correct? Thank you very much. Max On Sep 2, 2015, at 5:02 PM, Vitaly V. Chaban <vvcha...@gmail.com<mailto:vvcha...@gmail.com>> wrote: It is difficult to get a very wrong density, especially for relatively rigid compounds. In the meantime, deviations of density within 2% of the experimental value should be admitted acceptable. A better criterion is to compare self-diffusion or viscosity to the experiment. Another famous property for parametrization is heat of vaporization. On Wed, Sep 2, 2015 at 3:22 PM, Ebert Maximilian <m.eb...@umontreal.ca<mailto:m.eb...@umontreal.ca>> wrote: Thanks for the reply. I think I found relatively good atom types for iso propanol and derived the partial charges using antechamber and red server. I next check the density of pure iso propanol and used the closest definition to the real value. Iso propanol is used as co-solvent with water with a water:iso propanol ration of 90:10. I will just use my derived parameters then. Thanks for your replies. Max On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban <vvcha...@gmail.com<mailto:vvcha...@gmail.com>> wrote: Normally, this sort of things is done via mechanical combining of the known groups -- CH3, -CH, OH -- from the force field. If your goal is to increase accuracy for pure 2-propanol per se, then play with the distribution of electronic density between OH and CH. If 2-propanol is to be used as a solvent for somwthing else, this does ultimately not pay off. On Wed, Sep 2, 2015 at 11:42 AM, Ebert Maximilian <m.eb...@umontreal.ca<mailto:m.eb...@umontreal.ca>> wrote: I saw the papers you mentioned but one is a not clear how they parameterized, one is missing the supporting material and the last is not showing the parameters they used. I will check with the initial paper of Jorgensen again but if I recall it correctly he mentioned some problems with iso-propanol. strange that such a common organic solvent is not easily accessible for OPLS. thanks for your help johnny! Max On Sep 1, 2015, at 11:41 PM, Johnny Lu <johnny.lu...@gmail.com<mailto:johnny.lu...@gmail.com>> wrote: that was by google. I haven't parametrized forcefields. did they just put the pieces in http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work for 2-propanol? On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu <johnny.lu...@gmail.com<mailto:johnny.lu...@gmail.com>> wrote: Not sure if those are for 2-propanol as a liquid or interaction between 2-propanol and protein. from googling "2 propanol opls/aa" 1. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids The parameters are in the supporting info. Seems not exactly 2-propanol. But it has parameter for organic liquids. "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols" http://pubs.acs.org/doi/abs/10.1021/ja9621760 2. A statistical model of hydrogen bond networks in liquid alcohols http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf 3. Parameterization of OPLS–AA Force Field for the Conformational Analysis of Macrocyclic Polyketides https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: Dear list, I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA format. Before deriving my own I thought it would be best to ask first. I saw some posts that people used 2-pro
Re: [gmx-users] OPLS/AA parameters for 2-propanol
Thanks for the reply. I think I found relatively good atom types for iso propanol and derived the partial charges using antechamber and red server. I next check the density of pure iso propanol and used the closest definition to the real value. Iso propanol is used as co-solvent with water with a water:iso propanol ration of 90:10. I will just use my derived parameters then. Thanks for your replies. Max > On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban <vvcha...@gmail.com> wrote: > > Normally, this sort of things is done via mechanical combining of the > known groups -- CH3, -CH, OH -- from the force field. > > If your goal is to increase accuracy for pure 2-propanol per se, then > play with the distribution of electronic density between OH and CH. > > If 2-propanol is to be used as a solvent for somwthing else, this does > ultimately not pay off. > > > > > > > > >> On Wed, Sep 2, 2015 at 11:42 AM, Ebert Maximilian <m.eb...@umontreal.ca> >> wrote: >> I saw the papers you mentioned but one is a not clear how they >> parameterized, one is missing the supporting material and the last is not >> showing the parameters they used. I will check with the initial paper of >> Jorgensen again but if I recall it correctly he mentioned some problems with >> iso-propanol. >> >> strange that such a common organic solvent is not easily accessible for OPLS. >> >> thanks for your help johnny! >> >> Max >> >>> On Sep 1, 2015, at 11:41 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: >>> >>> that was by google. I haven't parametrized forcefields. >>> did they just put the pieces in >>> http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work >>> for 2-propanol? >>> >>> >>>> On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: >>>> >>>> Not sure if those are for 2-propanol as a liquid or interaction between >>>> 2-propanol and protein. >>>> from googling "2 propanol opls/aa" >>>> >>>> 1. Development and Testing of the OPLS All-Atom Force Field on >>>> Conformational Energetics and Properties of Organic Liquids >>>> The parameters are in the supporting info. >>>> Seems not exactly 2-propanol. But it has parameter for organic >>>> liquids. >>>> "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols" >>>> http://pubs.acs.org/doi/abs/10.1021/ja9621760 >>>> >>>> 2. A statistical model of hydrogen bond networks in liquid alcohols >>>> >>>> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf >>>> >>>> 3. Parameterization of OPLS–AA Force Field for the Conformational Analysis >>>> of Macrocyclic Polyketides >>>> https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf >>>> >>>> On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian <m.eb...@umontreal.ca> >>>> wrote: >>>> >>>>> Dear list, >>>>> >>>>> I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA >>>>> format. Before deriving my own I thought it would be best to ask first. I >>>>> saw some posts that people used 2-propanol in OPLS but couldn’t find any >>>>> reference in google scholar. >>>>> >>>>> Thank you very much, >>>>> >>>>> Max >>>>> -- >>>>> 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-u
Re: [gmx-users] OPLS/AA parameters for 2-propanol
I saw the papers you mentioned but one is a not clear how they parameterized, one is missing the supporting material and the last is not showing the parameters they used. I will check with the initial paper of Jorgensen again but if I recall it correctly he mentioned some problems with iso-propanol. strange that such a common organic solvent is not easily accessible for OPLS. thanks for your help johnny! Max > On Sep 1, 2015, at 11:41 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > > that was by google. I haven't parametrized forcefields. > did they just put the pieces in > http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work > for 2-propanol? > > > On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > >> Not sure if those are for 2-propanol as a liquid or interaction between >> 2-propanol and protein. >> from googling "2 propanol opls/aa" >> >> 1. Development and Testing of the OPLS All-Atom Force Field on >> Conformational Energetics and Properties of Organic Liquids >> The parameters are in the supporting info. >> Seems not exactly 2-propanol. But it has parameter for organic >> liquids. >> "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols" >> http://pubs.acs.org/doi/abs/10.1021/ja9621760 >> >> 2. A statistical model of hydrogen bond networks in liquid alcohols >> >> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf >> >> 3. Parameterization of OPLS–AA Force Field for the Conformational Analysis >> of Macrocyclic Polyketides >> https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf >> >> On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian <m.eb...@umontreal.ca> >> wrote: >> >>> Dear list, >>> >>> I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA >>> format. Before deriving my own I thought it would be best to ask first. I >>> saw some posts that people used 2-propanol in OPLS but couldn’t find any >>> reference in google scholar. >>> >>> Thank you very much, >>> >>> Max >>> -- >>> 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] Create file topology in oplsaa
you can also look at this tutorial if you want to have starting point for generating topologies: http://www.esi.umontreal.ca/~pelletjo/gromacs/ max On Jul 21, 2015, at 9:52 AM, gozde ergin gozdeeer...@gmail.commailto:gozdeeer...@gmail.com wrote: Gromacs has OPLSAA force field. You can use pdb2gmx command. Also you can use topolbuild software. If you google it, you can easily find how to use it. On Tue, Jul 21, 2015 at 2:38 PM, Daniele Veclani danielevecl...@gmail.commailto:danielevecl...@gmail.com wrote: Dear users I'm trying to create a topology file for a molecule to oplsaa force fields How can I do this? I have read that I can do this with the program MKTOP but I can not use it. Is there a tutorial for this program? Best regards Daniele. -- 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.orgmailto: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.orgmailto: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] Cross-correlation map of protein residues
Dear list, I am looking for a gromacs tool which is able to calculate/draw a map of residues which are either in their motion correlated or anti correlated. first i thought i could just use g_covar with c-alpha and use the -xpma option but while reading previous mailing list posts people said that the atomic covariance matrix does not correlate motions. All posts I found where older and the script from the gromacs site for a g_covar tool which can calculate the correlation plot is from 2009. Therefore, i wanted to know if gromacs 5 is able to directly calculate the plot. if not does anybody know a straight forward way of doing so for a gromacs trajectory? thank you very much, max -- 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] Pressure Coupling in GROMACS
Hi Ashraf, from the gromacs website (http://www.gromacs.org/Documentation/Terminology/Berendsen): The distribution of temperatures and pressures (in the case of the thermostat and barostat, respectively) does not correspond to any known statistical mechanical ensemble. It is best applied during the early stages of equilibration, as it converges relatively quickly and can be useful for stabilizing systems that may be far from equilibrium. So you should ne use Berendsen for production only for equilibration. Check out one of those: http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling Max On Jun 8, 2015, at 9:10 AM, Jashimuddin Ashraf jashimuddin.ashra...@gmail.commailto:jashimuddin.ashra...@gmail.com wrote: Dear GROMACS users, I am new to GROMACS. My system contains only carbon nanotubes and inside my md.mdp file I have- . . Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1; @pressure coupling 1ps compressibility = 4.5e-5; ref_p= 1.0; @reference pressure . . whenever I run the grompp command, I get a warning called- Using Berendsen pressure coupling invalidates the true ensemble for the thermostat I looked up at the mail list where I found Parrinello-Rahman to be appropriate for the NPT simulations. But I intend to run production MD. Is this an error to be worried about? (I can obviously run simulations using maxwarn) I have another problem. When I simulated carbon nanotubes with water/ other molecules, the average pressure I observed from simulation (using g_energy command) had a good agreement with the ref_p. But now the average pressure becomes independent of my ref_p. This is a problem that is bugging me for a long time. How can I resolve this? Thanks in advance. -- 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.orgmailto: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] OPLS definition of Phenyl palmitate
Thanks for your response. First of all I must say it is a bit strange that OPLS has the atom types of phenyl ester but not the corresponding dihedral angels to support it. But I see your point but could you elaborate on how I could evaluate this? How can I calculate those profiles? Thanks, Max On Jun 7, 2015, at 9:49 AM, Justin Lemkul jalem...@vt.edumailto:jalem...@vt.edu wrote: On 6/5/15 6:08 PM, Ebert Maximilian wrote: Hi, a small little update. I saw that CT OS C_2 O_2 and CT OS C_2 CT are defined OPLS/AA. I used these parameters now to define CA OS C_2 O_2 and CA OS C_2 CT in OPLS/AA. Any thoughts on that? I really have difficulties to visualize dihedral angles and I am not sure if this would actually give roughly the same geometry or not. The determining factor is whether or not the QM and MM energy profiles match as those dihedrals are rotated. -Justin Thanks and have a good weekend. Max On Jun 5, 2015, at 4:38 PM, Ebert Maximilian m.eb...@umontreal.camailto:m.eb...@umontreal.ca wrote: Dear list, I ran into some problem to define the topology of phenyl palmitate. My main problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of the molecule without hydrogen (I hope it turns out to be readable in the email): O17 || C21 - C20 C16 (C)n /\ / \ / \ C22 C19 - O18 C15C1 \/ C23 - C24 I think I defined the atom types correctly: [ atoms ] ; nr type resi res atom cgnr charge mass 1 opls_768 1 PNR C224-0.1952 12.01100 2 opls_145 1 PNR C215-0.0500 12.01100 3 opls_145 1 PNR C206-0.1550 12.01100 4 opls_145 1 PNR C237-0.0500 12.01100 5 opls_145 1 PNR C248-0.1550 12.01100 6 opls_472 1 PNR C199 0.1591 12.01100 7 opls_473 1 PNR O18 10-0.3732 15.99940 8 opls_465 1 PNR C16 11 0.6491 12.01100 9 opls_466 1 PNR O17 12-0.5100 15.99940 10 opls_136 1 PNR C15 13-0.1264 12.01100 11 opls_136 1 PNR C14 14-0.0804 12.01100 12 …. The problem is now in the ester since there is no dihedral definition of CA OS C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 which is Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl ester). Do I understand 472 correctly? How can I resolve the missing two dihedral angles? I also wanted to know if somebody has an idea what is meant by: AA C: esters - for R on C=O, use #280-#282 of the atom type opls_465. Do I need in this case to assign opls_280 to C15 and opls_282 to the corresponding hydrogens since they are the R of the ester? Thank you very much for your advice, Max -- 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.orgmailto:gmx-users-requ...@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 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edumailto:jalem...@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-requ...@gromacs.orgmailto: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] OPLS definition of Phenyl palmitate
Dear list, I ran into some problem to define the topology of phenyl palmitate. My main problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of the molecule without hydrogen (I hope it turns out to be readable in the email): O17 || C21 - C20 C16 (C)n /\ / \ / \ C22 C19 - O18 C15C1 \/ C23 - C24 I think I defined the atom types correctly: [ atoms ] ; nr type resi res atom cgnr charge mass 1 opls_768 1 PNR C224-0.1952 12.01100 2 opls_145 1 PNR C215-0.0500 12.01100 3 opls_145 1 PNR C206-0.1550 12.01100 4 opls_145 1 PNR C237-0.0500 12.01100 5 opls_145 1 PNR C248-0.1550 12.01100 6 opls_472 1 PNR C199 0.1591 12.01100 7 opls_473 1 PNR O18 10-0.3732 15.99940 8 opls_465 1 PNR C16 11 0.6491 12.01100 9 opls_466 1 PNR O17 12-0.5100 15.99940 10 opls_136 1 PNR C15 13-0.1264 12.01100 11 opls_136 1 PNR C14 14-0.0804 12.01100 12 …. The problem is now in the ester since there is no dihedral definition of CA OS C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 which is Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl ester). Do I understand 472 correctly? How can I resolve the missing two dihedral angles? I also wanted to know if somebody has an idea what is meant by: AA C: esters - for R on C=O, use #280-#282 of the atom type opls_465. Do I need in this case to assign opls_280 to C15 and opls_282 to the corresponding hydrogens since they are the R of the ester? Thank you very much for your advice, Max -- 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] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
I just finished to write a tutorial on how to parameterize an organic molecule in OPLS/AA using MKTop, TopolGen, ACPYPE, RED Server, antechamber and Schrodinger Maestro. I also added a part to valid the charges and the final topology. Any comments, corrections and improvements are more than welcome. http://www.esi.umontreal.ca/~pelletjo/gromacs/derive01.html I reference Justin’s tutorials a lot. Thanks again to you for taking so much time and share them with the community. You make GROMACS so much more accessible for new users. Max On May 29, 2015, at 2:53 PM, Ebert Maximilian m.eb...@umontreal.camailto:m.eb...@umontreal.ca wrote: I continued to define good partial charges using the tools suggested. I found that the combination of Maestro + ffconv or mktop, ACPYPE and antechamber + mktop have all advantages and disadvantages depending on the organic molecule. for instance for acetone with maestro and mktop i could achieve the same topology as virtual chemistry. I next tried to generate a topology for iso-propanol. Here ACPYPE charges with the mktop atom types gave the closes density to the experimental one. I also tried to calculate the heat capacity with Cp and Cv to compare it with the literature. My box is 2.3x2.3x2.3nm large and has about 150 molecules of the organic solvent. After 1ns of NPT i get values which are 5x higher than the literature value (gmx energy -f npt.edr -fluct_props -nmol 100). I also tried a box 5x5x5nm with over 1000 molecules and got the same result. Any idea why the simulation using OPLS AA FF is so far of when it comes to the heat capacity? thanks max On May 28, 2015, at 9:19 AM, Ebert Maximilian m.eb...@umontreal.camailto:m.eb...@umontreal.ca wrote: Thanks Justin and Kalev this brings me already much further. I tried ffld_server and it works just fine. However, it is like a black box. I can’t really find the documentation on how ffld_server gets the charges. Do you know where to find the documentation? Thanks On May 28, 2015, at 2:22 AM, Kalev Takkis kalev.tak...@gmail.commailto:kalev.tak...@gmail.com wrote: If you're after OPLS topologies for GROMACS then one way to derive them is via Schrödinger's Maestro (free academics version is sufficient) and Andrey Frolov's ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can create a force field represesentation of a molecule with the former (described here http://www.schrodinger.com/kb/809) and then convert it to GROMACS format with the latter. All the best, Kalev On 28 May 2015 at 03:37, Mohd Farid Ismail mohd.farid.ism...@yandex.commailto:mohd.farid.ism...@yandex.com wrote: You can try R.E.D. Server. It has more charge models (I don't know whether that will help). Also, IMO, one should target the density and the static dielectric constant when it comes to VDW and partial charges. I saw a recent paper that might be of interest to you http://pubs.acs.org/doi/abs/10.1021/jp3002383 -- Mohd Farid Ismail 28.05.2015, 05:13, Ebert Maximilian m.eb...@umontreal.ca: I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters? Thank you very much, max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual
Re: [gmx-users] error group protein not found
Hi, if there is a protein in your system you should have protein as standard group. Maybe you use a template mdp file in which the temperature coupling group is protein. if you have no protein in your simulation check the mdp files for tc-grps and adjust accordingly. Max On Jun 3, 2015, at 3:07 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: Hello, In your command line you do not specify an index file. Maybe you need to generate one. Check out usage of make_ndx. Hope this helps Victor 2015-06-03 13:41 GMT-05:00 marzieh dehghan dehghanmarz...@gmail.com: Hi every body I create a covalent bond and now I want to held MD by gromacs, after holding the following command : grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr I confornted to an error: Fatal error: Group Protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. please let me know how can I solve this problem. I am looking forward to getting your answer thanks a lot -- *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- 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] Looking for FF parameters for bivalent metals and oxoguanine
Hi Timofey, did you check http://ambermd.org/tutorials/basic/tutorial4b/ or https://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs cheers, Max On Jun 3, 2015, at 12:24 AM, Timofey Tyugashev tyugas...@niboch.nsc.rumailto:tyugas...@niboch.nsc.ru wrote: I'm investigating several protein-DNA systems with AMBER 99SB force field . Some of them involve 8-oxoG lesions and metal-dependent enzymes. Is there any reliable calculated parameters for them or any reliable and reasonably quick way to derive them? -- 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.orgmailto: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] Questions about the topology file format
Hi there, I have two quick questions about the topology file format which I couldn’t find in the documentary. The semi-colon is giving me some headache. Is it always a comment which is written after? First: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 opls_135 1 IPAC11-0.111600 12.01100 ; qtot -0.112 CT is qtot and CT used for anything and is it interpreted since it is after the ; Second: [ bonds ] ; ai aj funct r k 1 2 1 ;1.5350e-012.5363e+05 ; C1 - C2 CT - CT are the values for r and k here used since they are after the ; and what is C1-C2 and CT-CT used for and why another ;? Thank you very much for clarification. Max -- 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] Adding a substrate into protein-lipid bilayer system
Hi Dewey, maybe a little bit off topic but your description of the system reminded me of a paper I read a couple of years ago. Do you know about the ABF method and the work of Lamoureux et al? (http://pubs.acs.org/doi/abs/10.1021/ja300129x) maybe worth checking because it sounds like the simulation you want to execute (even though they don’t use GROMACS). Max On May 31, 2015, at 4:17 PM, MPI mpi...@gmail.commailto:mpi...@gmail.com wrote: Dear Users, I have a protein-lipid bilayer system and this protein is an ion channel. I would like to force a substrate eg, ammonia (NH3) passing through this channel. I wonder when it is appropriate to add NH3 into the system and how to setup the control of temperature coupling in thermostats. For example, 1. add NH3 first with the protein and then embed protein-NH3 into the lipid or 2. embed the protein into lipid with an equilibration, followed by adding NH3 into the system Also, if the substrate has a charge, which order is preferred ? Thanks, Dewey -- 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.orgmailto: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] trjcat issue
Hi, try to set the time manually. It fixed the problem for me (-settime). Max On May 28, 2015, at 4:43 AM, Giannis Gl igalda...@gmail.com wrote: Dear all, I tried to concatenate two trajectories using the comand trjcat -f Trajectory_total.xtc md26_out.xtc -o Trajectory_total_full.xtc The process ended normaly: Reading frame 1 time 3000310.000 Summary of files and start times used: FileStart time Time step - Trajectory_total.xtc0.000 ps 10.000 ps md26_out.xtc 3000300.000 ps 10.000 ps Reading frame 0 time0.000 Continue writing frames from Trajectory_total.xtc t=0 ps, frame=0 Reading frame 314000 time 314.000- frame 30 time 300.000 ps Reading frame 0 time 3000300.000 lasttime 3.00029e+06 Continue writing frames from md26_out.xtc t=3.0003e+06 ps, frame=300030 - frame 314720 time 3147200.000 ps - frame 314030 time 3140300.000 ps Last frame written was 314720, time 3147200.00 ps But when I tried to see any frame after 3300.000 ps I ended up with an error like Fatal error: Specified frame (time 30003000.00) doesn't exist or file corrupt/inconsistent. What have I done wrong? -- 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] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Hi, thanks diana for your input and for the review. I never used GROMOS so far and I feel less comfortable using an unknown FF at this point. I am writing a tutorial on how to parameterize organic molecules right now and will publish it this week. Maybe you can comment on the strategy to have a relatively clean and broad approach. I was wondering which physical-chemical properties did you use to verify your definition? So far I am looking at density, Cp and Cv. Thanks! Max On May 28, 2015, at 5:15 AM, Diana Lousa dlo...@itqb.unl.pt wrote: Hi, Our group has done many studies using enzymes in organic solvents (with different amounts of water) and we always used the GROMOS FF for the proteins and compatible parameters for the solvents. We can find a review of enzyme simulations in nonaqueous solvents here: http://pubs.rsc.org/en/Content/ArticleLanding/2013/CP/c3cp51761f#!divAbstract The parameters that we used for different solvents were able to reproduce their physical-chemical properties. I can also tell you that from our experience the latest GROMOS FF are able to reproduce the structural properties of small peptides and proteins also seem to be quite stable when these FF are used. Thus, using GROMOS 54A7 for the protein and compatible parameters for organic solvents can be a good choice. However, if you want to use PME for long-range electrostatics, you have to test if these parameters work in these conditions, because they were developed to be used with RF. On Thu, May 28, 2015 at 7:22 AM, Kalev Takkis kalev.tak...@gmail.com wrote: If you're after OPLS topologies for GROMACS then one way to derive them is via Schrödinger's Maestro (free academics version is sufficient) and Andrey Frolov's ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can create a force field represesentation of a molecule with the former (described here http://www.schrodinger.com/kb/809) and then convert it to GROMACS format with the latter. All the best, Kalev On 28 May 2015 at 03:37, Mohd Farid Ismail mohd.farid.ism...@yandex.com wrote: You can try R.E.D. Server. It has more charge models (I don't know whether that will help). Also, IMO, one should target the density and the static dielectric constant when it comes to VDW and partial charges. I saw a recent paper that might be of interest to you http://pubs.acs.org/doi/abs/10.1021/jp3002383 -- Mohd Farid Ismail 28.05.2015, 05:13, Ebert Maximilian m.eb...@umontreal.ca: I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters? Thank you very much, max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_280 1 LIG C 1 0.47 12.011 2 opls_135 1 LIG C 2 -0.18 12.011 3 opls_135 1 LIG C 3 -0.18 12.011 4 opls_281 1 LIG O 4 -0.47
Re: [gmx-users] Volume of active site
Hi Raja, you could also give 3V a try: http://3vee.molmovdb.org Cheers, Max On Jun 1, 2015, at 11:12 AM, Erik Marklund erik.markl...@chem.ox.ac.ukmailto:erik.markl...@chem.ox.ac.uk wrote: Dear Raja, Depending on how you define that volume, you may achieve what you want through clever use of g_sas -tv (gmx sas nowadays). Kind regards, Erik On 1 Jun 2015, at 15:19, Raj D gromacs.fo...@gmail.commailto:gromacs.fo...@gmail.com wrote: Dear user, I have completed a set of MD simulations of mutants and wild type of a protein complexed with its substrate in its active site , I have inferred that the active sites of all mutant enzymes have gone enlarged relative to wild type which is consistent with our kinetic study of the mutants, the Km values are so high for all mutant enzymes and I would like quantify the volume of the active site comprising a set of 17 active site residues ..Is there any direct or indirect tool in gromacs to compute the volume like that ? Or any free tools available . Regards, Raja -- 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.orgmailto: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.orgmailto: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] VMD Visulazation
Hey Victor, check http://manual.gromacs.org/current/programs/gmx-trjconv.html you probably need -ur and -pbc Cheers, Max On Jun 1, 2015, at 1:45 PM, Victor Ma victordsmag...@gmail.commailto:victordsmag...@gmail.com wrote: Hello Justin, Thanks a lot for the quick response. So I first load the .gro file from the previous step which is my initial coordinate file, I then loaded the .trr file. But I am getting some wired image. Please see attachment. Thank you. Victor -- 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.orgmailto: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] Rule for atom names in GROMACS
Hi there, While building my own topology I was wondering if the atom name is only used to link .gro atoms with .top entries. The behaviour of an atom is defined by the atom type and the atom name should not have any effect on the simulation right? So if I choose an atom name for a carbon as C, C11 or C2 the outcome should be the same as long as the atom has the same name in .gro and .top and the same type. Am I correct here? So atom names are used to link .top and .gro and later in visualization softwares like VMD to place a carbon atom in the GUI instead of something else. Correct? Finally I was wondering if the atom name needs to be unique within a molecule. Thanks for the clarification, Max -- 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] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
I continued to define good partial charges using the tools suggested. I found that the combination of Maestro + ffconv or mktop, ACPYPE and antechamber + mktop have all advantages and disadvantages depending on the organic molecule. for instance for acetone with maestro and mktop i could achieve the same topology as virtual chemistry. I next tried to generate a topology for iso-propanol. Here ACPYPE charges with the mktop atom types gave the closes density to the experimental one. I also tried to calculate the heat capacity with Cp and Cv to compare it with the literature. My box is 2.3x2.3x2.3nm large and has about 150 molecules of the organic solvent. After 1ns of NPT i get values which are 5x higher than the literature value (gmx energy -f npt.edr -fluct_props -nmol 100). I also tried a box 5x5x5nm with over 1000 molecules and got the same result. Any idea why the simulation using OPLS AA FF is so far of when it comes to the heat capacity? thanks max On May 28, 2015, at 9:19 AM, Ebert Maximilian m.eb...@umontreal.ca wrote: Thanks Justin and Kalev this brings me already much further. I tried ffld_server and it works just fine. However, it is like a black box. I can’t really find the documentation on how ffld_server gets the charges. Do you know where to find the documentation? Thanks On May 28, 2015, at 2:22 AM, Kalev Takkis kalev.tak...@gmail.com wrote: If you're after OPLS topologies for GROMACS then one way to derive them is via Schrödinger's Maestro (free academics version is sufficient) and Andrey Frolov's ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can create a force field represesentation of a molecule with the former (described here http://www.schrodinger.com/kb/809) and then convert it to GROMACS format with the latter. All the best, Kalev On 28 May 2015 at 03:37, Mohd Farid Ismail mohd.farid.ism...@yandex.com wrote: You can try R.E.D. Server. It has more charge models (I don't know whether that will help). Also, IMO, one should target the density and the static dielectric constant when it comes to VDW and partial charges. I saw a recent paper that might be of interest to you http://pubs.acs.org/doi/abs/10.1021/jp3002383 -- Mohd Farid Ismail 28.05.2015, 05:13, Ebert Maximilian m.eb...@umontreal.ca: I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters? Thank you very much, max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_280 1 LIG C 1 0.47 12.011 2 opls_135 1 LIG C 2 -0.18 12.011 3 opls_135 1 LIG C 3 -0.18 12.011 4 opls_281 1 LIG O 4 -0.47 15.9994 5 opls_282 1 LIG H 5 0.06 1.008 6 opls_282 1 LIG H 6 0.06 1.008 7 opls_282 1 LIG
Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Thanks Justin and Kalev this brings me already much further. I tried ffld_server and it works just fine. However, it is like a black box. I can’t really find the documentation on how ffld_server gets the charges. Do you know where to find the documentation? Thanks On May 28, 2015, at 2:22 AM, Kalev Takkis kalev.tak...@gmail.com wrote: If you're after OPLS topologies for GROMACS then one way to derive them is via Schrödinger's Maestro (free academics version is sufficient) and Andrey Frolov's ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can create a force field represesentation of a molecule with the former (described here http://www.schrodinger.com/kb/809) and then convert it to GROMACS format with the latter. All the best, Kalev On 28 May 2015 at 03:37, Mohd Farid Ismail mohd.farid.ism...@yandex.com wrote: You can try R.E.D. Server. It has more charge models (I don't know whether that will help). Also, IMO, one should target the density and the static dielectric constant when it comes to VDW and partial charges. I saw a recent paper that might be of interest to you http://pubs.acs.org/doi/abs/10.1021/jp3002383 -- Mohd Farid Ismail 28.05.2015, 05:13, Ebert Maximilian m.eb...@umontreal.ca: I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters? Thank you very much, max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_280 1 LIG C 1 0.47 12.011 2 opls_135 1 LIG C 2 -0.18 12.011 3 opls_135 1 LIG C 3 -0.18 12.011 4 opls_281 1 LIG O 4 -0.47 15.9994 5 opls_282 1 LIG H 5 0.06 1.008 6 opls_282 1 LIG H 6 0.06 1.008 7 opls_282 1 LIG H 7 0.06 1.008 8 opls_282 1 LIG H 8 0.06 1.008 9 opls_282 1 LIG H 9 0.06 1.008 10 opls_282 1 LIG H10 0.06 1.008 antechamber AM1-BCC derived [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_280 1 ACN C110.56 12.011 2 opls_281 1 ACN O11 -0.52 15.9994 3 opls_135 1 ACN C22 -0.20 12.011 4 opls_135 1 ACN C33 -0.20 12.011 5 opls_282 1 ACN H120.06 1.008 6 opls_282 1 ACN H220.06 1.008 7 opls_282 1 ACN H320.06 1.008 8 opls_282 1 ACN H430.06 1.008 9 opls_282 1 ACN H530.06 1.008 10 opls_282 1 ACN H630.06 1.008 The atom types
Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
the density and see how it matches with reality. What do you think about this approach? What would have been a better way? How can I make sure that the charges are correct? Thanks for your input. Max On May 27, 2015, at 11:54 AM, Ebert Maximilian m.eb...@umontreal.camailto:m.eb...@umontreal.ca wrote: Hi there, I am about to setup a water:organic solvent mixture with a protein. I found many organic molecules on http://virtualchemistry.org with definitions for the OPLS FF. However, some are missing so I would need to derive the parameters myself. Before going into more details I was wondering if OPLS is to be preferred if organic solvent is present or can AMBER also be used? It seems that using ACPYPE with AMBER is much more accessible than using any other method to derive the parameters for organic molecules. Thanks for your advice. -- 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.orgmailto: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] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Hi there, I am about to setup a water:organic solvent mixture with a protein. I found many organic molecules on http://virtualchemistry.org with definitions for the OPLS FF. However, some are missing so I would need to derive the parameters myself. Before going into more details I was wondering if OPLS is to be preferred if organic solvent is present or can AMBER also be used? It seems that using ACPYPE with AMBER is much more accessible than using any other method to derive the parameters for organic molecules. Thanks for your advice. -- 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] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters? Thank you very much, max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_280 1 LIG C 1 0.47 12.011 2 opls_135 1 LIG C 2 -0.18 12.011 3 opls_135 1 LIG C 3 -0.18 12.011 4 opls_281 1 LIG O 4 -0.47 15.9994 5 opls_282 1 LIG H 5 0.06 1.008 6 opls_282 1 LIG H 6 0.06 1.008 7 opls_282 1 LIG H 7 0.06 1.008 8 opls_282 1 LIG H 8 0.06 1.008 9 opls_282 1 LIG H 9 0.06 1.008 10 opls_282 1 LIG H10 0.06 1.008 antechamber AM1-BCC derived [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_280 1 ACN C110.56 12.011 2 opls_281 1 ACN O11 -0.52 15.9994 3 opls_135 1 ACN C22 -0.20 12.011 4 opls_135 1 ACN C33 -0.20 12.011 5 opls_282 1 ACN H120.06 1.008 6 opls_282 1 ACN H220.06 1.008 7 opls_282 1 ACN H320.06 1.008 8 opls_282 1 ACN H430.06 1.008 9 opls_282 1 ACN H530.06 1.008 10 opls_282 1 ACN H630.06 1.008 The atom types were guessed correctly by mktop and also the charge groups make sense I think. So far so good. I realize some differences between the two topologies. First the mktop topology also includes FF constants for the different bonds and angles: [ bonds ] 1 2 1 0.121 476976.0 1 3 1 0.151 265265.6 1 4 1 0.151 265265.6 3 5 1 0.109 284512.0 3 6 1 0.109 284512.0 3 7 1 0.109 284512.0 4 8 1 0.109 284512.0 4 9 1 0.109 284512.0 4 10 1 0.109 284512.0 [ angles ] 1 3 5 1 109.460 292.880 1 3 6 1 109.473 292.880 1 3 7 1 109.484 292.880 1 4 8 1 109.466 292.880 1 4 9 1 109.435 292.880 1 4 10 1 109.477 292.880 2 1 3 1 119.985 669.440 2 1 4 1 119.985 669.440 3 1 4 1 120.029 585.760 5 3 6 1 109.445 276.144 5 3 7 1 109.464 276.144 6 3 7 1 109.502 276.144 8 4 9 1 109.483 276.144 8 4 10 1 109.504 276.144 9 4 10 1 109.462 276.144 compared to the virtual chemistry file: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 2 5 1 2 6 1 2 7 1 3 8 1 3 9 1 310 1 [ angles ] ; aiajak funct
Re: [gmx-users] Ligand covalently bound to protein: Best practice
Thanks for your comment and sorry for my weird english. I must have been in my thoughts :). I was also wondering if I attach covalently a protein to another protein or a large organic molecule through a residue in the middle of the sequence my approach would not work. Does anyone have a suggestion how setup a system like this? Thanks, Max On May 21, 2015, at 4:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/15 4:30 PM, Ebert Maximilian wrote: Hi there, I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice? Sounds reasonable. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@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-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] Ligand covalently bound to protein: Best practice
Hi there, I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice? Thanks very much, Max -- 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] g_hbond never shows hbond with HW2
Dear list, I discovered something strange today. In my hbond search i find only HW1 of the water forming a hydrogen bond as donor hydrogen and never HW2. Is this due to the fact that I am using SPC water? I can see the atom IDs of HW2 in the [ donors_hydrogens_Water ] entry in the ndx file. So technically GROMACs searched for HW2 donor connections but never finds any. However, thousands of hbonds are found with HW1. Any thoughts on that? Thanks, Max -- 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] Can't find the reference in hbond calculation between the map and the index file
Hey Justin, Thank you for your answer. I wanted just to be sure since other programs define H-bonds slightly different so identification of each line is a bit complicated when comparing frame by frame. I was trying to find the exact same number of H-bonds for instance in pymol but I could never get the definition about right so that gromacs and pymol find exactly the same hbonds. thanks for the offer I also wrote a program now to determine hydrogen bond networks across one water molecule. not sure if this can be any helpful to anyone. if so just contact me. have a good day, Max On Apr 17, 2015, at 2:18 PM, Justin Lemkul jalem...@vt.edumailto:jalem...@vt.edu wrote: On 4/17/15 2:02 PM, Ebert Maximilian wrote: Hey List, I already got a nice idea from Erik how to find residues bridged by a water molecule by using the hbond tool and the map and index file. I still have a question regarding the index. If I am not mistaken the first entry of bond registry entry: [ hbonds_Water-r_216_r_244 ] 4216 4217 3342 7225 7226 2962 should correspond to the last entry in the xpm file matrix: /* y-axis: 0 1 2 3 4 5 6 7 8 9 10 11 12 */ oo o ooo oo oo ooo ooo ooo o oo o o ooo ooo oo oo o “, oo “ and hence the last bond entry (7225 7226 2962) corresponds to the line beneath the y-axis entry? Just to be sure. Is this correct? Couldn’t find any hint what is described by Hydrogen Bond Index in the map file. Yes, the .ndx and .xpm are backwards with respect to one another from the top-down perspective. I wrote a script that does all the mapping if you want (parse_hbmap.pl) at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html It requires some modification of the .ndx file (you have to kill off all the lines that don't correspond to the actual hydrogen bonds) but it may save you some time to look through it. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edumailto:jalem...@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-requ...@gromacs.orgmailto: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] Checking the existence of a hydrogen bond network
Dear list, I am trying to find a possibility with standard gromacs tools to verify in every frame if two residues are interconnected through a hbonds with a water molecule. My initial idea was to evaluate the hbonds of both residues per frame and write a small bash script looking for frames in which both residues hbonded with the same water molecule. However, I could’t find an option in gmx hbond to write out the hbonds per frame except for the number of hbonds per frame and a file with all partners. Before starting to have to loop over every frame individually and start gmx hbond as often as the number of frames I wanted to know if there is an easier approach to what I want to do. Basically I want to know how long this bridge existed over the course of the simulation. Thank you very much, Max -- 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] Checking the existence of a hydrogen bond network
Hey Erik, Just wanted to thank you. This is exactly what I was looking for. Never looked at the end of the ndx file. Just a question regarding the index. If I am not mistaken the first entry of bond registry entry: [ hbonds_Water-r_216_r_244 ] 4216 4217 3342 7225 7226 2962 should correspond to the last entry in the xpm file matrix: /* y-axis: 0 1 2 3 4 5 6 7 8 9 10 11 12 */ oo o ooo oo oo ooo ooo ooo o oo o o ooo ooo oo oo o “, oo “ and hence the last bond entry (7225 7226 2962) corresponds to the line beneath the y-axis entry? Just to be sure. Have a great day, Max On Apr 16, 2015, at 11:28 AM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Max, You will need to use the -hbm and -hbn options to generate the existance function for all hydrogen bonds over time. Parsing those files requires a bit of work, but is certainly doable. Kind regards, Erik On 16 Apr 2015, at 12:59, Ebert Maximilian m.eb...@umontreal.ca wrote: Dear list, I am trying to find a possibility with standard gromacs tools to verify in every frame if two residues are interconnected through a hbonds with a water molecule. My initial idea was to evaluate the hbonds of both residues per frame and write a small bash script looking for frames in which both residues hbonded with the same water molecule. However, I could’t find an option in gmx hbond to write out the hbonds per frame except for the number of hbonds per frame and a file with all partners. Before starting to have to loop over every frame individually and start gmx hbond as often as the number of frames I wanted to know if there is an easier approach to what I want to do. Basically I want to know how long this bridge existed over the course of the simulation. Thank you very much, Max -- 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] Correlation of dynamics between pairs of residues
Thanks for taking the time to answer. However, I don’t really understand why having the same axis basically (so from -2 to 2 nm^2 for example) would defy the purpose of the analysis. Could you explain that? I guess your hint with open source is that i could check how the covara is calculated and do it on my own using the .dat ascii file? Do you know where the function is in the code? Thanks, Max On Mar 23, 2015, at 9:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/23/15 3:43 PM, Ebert Maximilian wrote: Hi Justin, thanks for your answer. gmx covar is really helpful and does what I was looking for.I have 3 replicates of the simulation and wanted now to compare the covariance and maybe calculate an average of the 3. The covara output is what I am looking for but the file created is more or less a picture and not really the data anymore. In addition, the scale of + and 0 nm^2 is not the same in each of the 3 output of the simulation so it is hard to compare. Is there a way to set min and max values for nm^2? Can I find an explanation how the data was calculated using the dat file i can generate using gmx covar? One approach would be to simply pool the trajectories and run gmx covar once. That will do the analysis over all of your trajectories and you no longer have this issue. But there is no way to control what the min and max values are; that sort of defeats the purpose of the analysis. As for the explanation, that's why GROMACS is open source :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@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-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] Correlation of dynamics between pairs of residues
Hi Justin, thanks for your answer. gmx covar is really helpful and does what I was looking for.I have 3 replicates of the simulation and wanted now to compare the covariance and maybe calculate an average of the 3. The covara output is what I am looking for but the file created is more or less a picture and not really the data anymore. In addition, the scale of + and 0 nm^2 is not the same in each of the 3 output of the simulation so it is hard to compare. Is there a way to set min and max values for nm^2? Can I find an explanation how the data was calculated using the dat file i can generate using gmx covar? Thank you very much, Max On Mar 12, 2015, at 8:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/12/15 6:20 PM, Ebert Maximilian wrote: Dear list, I am looking for a tool in gromacs to generate a map of residues pairs to indicate wether the dynamic/movement is correlated or anti correlated. Which tool is able to generate such an output? gmx covar will plot the covariance matrix for all atom pairs (3N x 3N), but you can map that to residues. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@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-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] Cosine content of an eigenvector in PCA after 100ns still 0.9
Hi Tsjerk, thanks for your reply. Can you explain this sentence again please: Not having a full set of cosines with periods equal to half the pc index just means you're not simulating gas or liquid. The simulation runs already for 500ns and I analyzed 100ns from 400 to 500ns. How can a simple protein system not be equilibrated yet? Max On Jan 15, 2015, at 3:52 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Max, The cosine content is a rather nonsensical parameter. HOWEVER, having a cosine content with 1/2 period that high one ANY eigenvector is indicative of unidirectional motion (a.k.a. conformational change/drift). That cosine contents with other periods on other eigenvectors is low is meaningless. Not having a full set of cosines with periods equal to half the pc index just means you're not simulating gas or liquid. In short, your system is not equilibrated. Cheers, Tsjerk On Thu, Jan 15, 2015 at 3:43 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi there, I have one question regarding the cosine content of an eigenvector. I did a PCA and calculated the cosine content of the 10 main eigenvectors. Except for the first all are really low. However, the main eigenvector is still around 0.9 after 100ns simulation. I am pretty sure my system is equilibrated. Do you have any idea what might happen? Thank you very much, Max -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] g_rotacf lag time
Dear list, is there a way to define the lag time for the auto correlation function in g_rotacf? Thank you very much, Max -- 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] Log output of GPU accelerated GROMACS
Dear list, I was wondering why the log file does not always contains the same information. In one of my configurations I got the following information: GPU timings - Computing: Count Wall t (s) ms/step % - Pair list H2D 1251 0.5630.450 0.2 X / q H2D 50001 6.9980.140 2.9 Nonbonded F kernel 47500 212.1184.46686.7 Nonbonded F+ene k. 1250 9.3717.497 3.8 Nonbonded F+ene+prune k.1251 9.7597.801 4.0 F D2H 50001 5.8740.117 2.4 - Total244.6834.894 100.0 - Force evaluation time GPU/CPU: 4.894 ms/4.012 ms = 1.220 For optimal performance this ratio should be close to 1! But I never got this information in any other configuration using GPUs. Is this only part of the output if there is a problem with too much work for the GPU? Thank you very much, Max -- 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] Performance difference between MPI ranks and OpenMP
Hi list, I have another question regarding performance. Is there any performance difference if I start a process on a 8 CPU machine with 8 MPI ranks and 1 OpenMP or 4 MPI ranks an 2 OpenMP? Both should use the 8 CPUs right? Thank you very much, Max -- 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] Performance difference between MPI ranks and OpenMP
The reason I am asking is because I want to use two GPUs and 8 CPUs. So for now I have 2 MPI ranks and 4 OpenMP threads. Is there a way to have 8 MPI ranks but only use 2 GPUs? I also tried 8 MPI ranks with -gpu_id but it was about the same as 2 MPI ranks with 4 OpenMP. Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Donnerstag, 8. Januar 2015 15:48 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Performance difference between MPI ranks and OpenMP On 08 Jan 2015, at 15:38, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi list, I have another question regarding performance. Is there any performance difference if I start a process on a 8 CPU machine with 8 MPI ranks and 1 OpenMP or 4 MPI ranks an 2 OpenMP? Both should use the 8 CPUs right? Right, but there is a performance difference (try it out! :) Normally using just one layer of parallelization is fastest (less overhead), i.e. using just OpenMP threads or just MPI ranks. However, more than 8 or so OpenMP threads per rank seldom yield optimal performance, so that a hybrid parallelization approach makes sense in such situations. Carsten Thank you very much, Max -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] g_tune_pme_mpi on GPU cluster fails
I always read this few hundred atoms per core. But how is this in the context of a GPU? For instance we use the GTX580 with 512 cores. Do they count as cores? Because the system I am working on has 13,000 atoms. With 8 CPU cores and 2 GPUs (with a total of 1024 cores) how do I count this? Do I have 1032 cores for 13,000 atoms? Do I count them individually? 13,000/8 and 13,000/1024? So that if I would have more CPUs per node I could achieve better performance? Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Donnerstag, 8. Januar 2015 15:51 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails On 08 Jan 2015, at 15:32, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi Carsten, I was benchmarking my first system and I do not see any improvement in using more than one GPU node. Whether you see an improvement or not depends on the size of your system and the latency of your interconnect. If it is Gigabit Ethernet, it might be the bottleneck. In the end I think having a node dedicated as PME node would make sense after all since our GPU cluster only consists of 9 nodes. What do you mean with high parallelization? What do you consider high? If you have so many cores that you end up with just a few hundred atoms per core I would say. Carsten Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Mittwoch, 7. Januar 2015 17:04 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails Hi, there are two issues here: a) you must not start multiple copies of g_tune_pme, but a single one. g_tune_pme will by itself launch MPI-parallel mdrun processes (the path to the mdrun executable needs to be specified in the MDRUN environment variable, you might need to set others as well depending on your queueing system - read g_tune_pme -h. b) g_tune_pme can not (yet) automatically deal with GPU nodes. With GPUs, separate PME nodes will also only make sense at very high parallelization - how many of these nodes do you want to use in parallel? Carsten On 07 Jan 2015, at 15:11, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi there, I have again a question regarding our GPU cluster. I tried to g_tune_pme_mpi on the cluster. After starting it across 3 nodes I get the following errors: Command line: g_tune_pme_mpi -v -x -deffnm 1G68_run1ns -s ../run100ns.tpr Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Will test 1 tpr file. Will test 1 tpr file. Will test 1 tpr file. Will test 1 tpr file. [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13382] [[25869,1],0] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13385] [[25869,1],1] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13384] [[25869,1],2] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 . = PBS: job killed: walltime 3641 exceeded limit 3600 mpirun: killing job... [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],3] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],2] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],1] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) Any idea what is wrong? Thank you very much! Max -Ursprüngliche Nachricht
Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails
Hi Carsten, I was benchmarking my first system and I do not see any improvement in using more than one GPU node. In the end I think having a node dedicated as PME node would make sense after all since our GPU cluster only consists of 9 nodes. What do you mean with high parallelization? What do you consider high? Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Mittwoch, 7. Januar 2015 17:04 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] g_tune_pme_mpi on GPU cluster fails Hi, there are two issues here: a) you must not start multiple copies of g_tune_pme, but a single one. g_tune_pme will by itself launch MPI-parallel mdrun processes (the path to the mdrun executable needs to be specified in the MDRUN environment variable, you might need to set others as well depending on your queueing system - read g_tune_pme -h. b) g_tune_pme can not (yet) automatically deal with GPU nodes. With GPUs, separate PME nodes will also only make sense at very high parallelization - how many of these nodes do you want to use in parallel? Carsten On 07 Jan 2015, at 15:11, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi there, I have again a question regarding our GPU cluster. I tried to g_tune_pme_mpi on the cluster. After starting it across 3 nodes I get the following errors: Command line: g_tune_pme_mpi -v -x -deffnm 1G68_run1ns -s ../run100ns.tpr Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Will test 1 tpr file. Will test 1 tpr file. Will test 1 tpr file. Will test 1 tpr file. [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13382] [[25869,1],0] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13385] [[25869,1],1] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13384] [[25869,1],2] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 . = PBS: job killed: walltime 3641 exceeded limit 3600 mpirun: killing job... [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],3] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],2] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],1] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) Any idea what is wrong? Thank you very much! Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Ebert Maximilian Gesendet: Mittwoch, 7. Januar 2015 14:43 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Carsten, thanks again for your reply. The why our cluster is setup is that you ask for GPUs using the ppn command and not CPUs. Therefore, I put 4 there. But to rule out the possibility that someone is actually using the note I called for 7 GPUs (so the entire note) but with GPU id just assign the first 4 to GROMACS. I still get the same error. I also tried -gpu_id 00 or -gpu_id to change the CPU and to only use a single GPU but I always get: NOTE: You assigned GPUs to multiple MPI processes. --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_too ls/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable For more information and tips
[gmx-users] g_tune_pme_mpi on GPU cluster fails
Hi there, I have again a question regarding our GPU cluster. I tried to g_tune_pme_mpi on the cluster. After starting it across 3 nodes I get the following errors: Command line: g_tune_pme_mpi -v -x -deffnm 1G68_run1ns -s ../run100ns.tpr Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Reading file ../run100ns.tpr, VERSION 5.0.1 (single precision) Will test 1 tpr file. Will test 1 tpr file. Will test 1 tpr file. Will test 1 tpr file. [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13382] [[25869,1],0] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13382] [[25869,1],0] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13385] [[25869,1],1] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13385] [[25869,1],1] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 [ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file rml_oob_send.c at line 104 [ngpu-a4-06:13384] [[25869,1],2] could not get route to [[INVALID],INVALID] [ngpu-a4-06:13384] [[25869,1],2] ORTE_ERROR_LOG: A message is attempting to be sent to a process whose contact information is unknown in file base/plm_base_proxy.c at line 81 . = PBS: job killed: walltime 3641 exceeded limit 3600 mpirun: killing job... [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],3] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],2] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) [ngpu-a4-06:13356] [[25869,0],0]-[[25869,1],1] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) Any idea what is wrong? Thank you very much! Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Ebert Maximilian Gesendet: Mittwoch, 7. Januar 2015 14:43 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Carsten, thanks again for your reply. The why our cluster is setup is that you ask for GPUs using the ppn command and not CPUs. Therefore, I put 4 there. But to rule out the possibility that someone is actually using the note I called for 7 GPUs (so the entire note) but with GPU id just assign the first 4 to GROMACS. I still get the same error. I also tried -gpu_id 00 or -gpu_id to change the CPU and to only use a single GPU but I always get: NOTE: You assigned GPUs to multiple MPI processes. --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Error on rank 1, will try to stop all ranks Halting parallel program gmx_mpi on CPU 1 out of 4 -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Mittwoch, 7. Januar 2015 14:13 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Max, On 07 Jan 2015, at 11:36, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi Carsten, thanks for your answer. I tried what you described and it is basically working except for letting multiple MPI workers use one GPU. In my setup I use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1. This is how I start GROMACS: mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s ../run1ns.tpr and I submit this using: qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu why are you using ppn=4? Shouldn't that be 8? Now I get the following errors (the output is longer but to keep it shorter I omitted the rest): Using 8 MPI processes Using 1 OpenMP thread per MPI process 7 GPUs detected on host ngpu-a4-06: #0: NVIDIA GeForce GTX 580
Re: [gmx-users] Working on a GPU cluster with GROMACS 5
Hi Jiri, Yes this seems to be the problem. Thank you very much. The GPUs on this cluster are in the exclusive thread mode. I will ask the administrator if we can change this. Thank you very much! Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Jiri Kraus Gesendet: Mittwoch, 7. Januar 2015 14:58 An: gromacs.org_gmx-users@maillist.sys.kth.se Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Max, In which compute mode are the GPUs running? Do be able to share a GPU between multiple MPI ranks you either need to use the multi process service (MPS see: [1]) or let the GPUs run in default compute mode (see [2]). You can query the compute mode with nvidia-smi -q -d COMPUTE (see example output below) and change it with nvidia-smi -c DEFAULT. Changing the compute mode requires root. Hope this helps Jiri [1] https://docs.nvidia.com/deploy/pdf/CUDA_Multi_Process_Service_Overview.pdf [2] http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#compute-modes Example output of nvidia-smi -q -d COMPUTE: ==NVSMI LOG== Timestamp : Wed Jan 7 05:51:31 2015 Driver Version : 340.32 Attached GPUs : 6 GPU :04:00.0 Compute Mode: Default GPU :05:00.0 Compute Mode: Default GPU :08:00.0 Compute Mode: Default GPU :09:00.0 Compute Mode: Default GPU :83:00.0 Compute Mode: Default GPU :84:00.0 Compute Mode: Default Message: 5 Date: Wed, 7 Jan 2015 13:42:46 + From: Ebert Maximilian m.eb...@umontreal.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Message-ID: CAE65A26CFD123408751DCA75C2BA164255E0839@athens- cour.sim.umontreal.ca Content-Type: text/plain; charset=iso-8859-1 Hi Carsten, thanks again for your reply. The why our cluster is setup is that you ask for GPUs using the ppn command and not CPUs. Therefore, I put 4 there. But to rule out the possibility that someone is actually using the note I called for 7 GPUs (so the entire note) but with GPU id just assign the first 4 to GROMACS. I still get the same error. I also tried -gpu_id 00 or -gpu_id to change the CPU and to only use a single GPU but I always get: NOTE: You assigned GPUs to multiple MPI processes. --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs- 5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Error on rank 1, will try to stop all ranks Halting parallel program gmx_mpi on CPU 1 out of 4 -Urspr?ngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Mittwoch, 7. Januar 2015 14:13 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Max, On 07 Jan 2015, at 11:36, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi Carsten, thanks for your answer. I tried what you described and it is basically working except for letting multiple MPI workers use one GPU. In my setup I use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1. This is how I start GROMACS: mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s ../run1ns.tpr and I submit this using: qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu why are you using ppn=4? Shouldn't that be 8? Now I get the following errors (the output is longer but to keep it shorter I omitted the rest): Using 8 MPI processes Using 1 OpenMP thread per MPI process 7 GPUs detected on host ngpu-a4-06: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #6: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible 4 GPUs user-selected for this run. Mapping of GPUs to the 8 PP ranks in this node: #0, #0, #1
Re: [gmx-users] Working on a GPU cluster with GROMACS 5
Hi Carsten, thanks again for your reply. The why our cluster is setup is that you ask for GPUs using the ppn command and not CPUs. Therefore, I put 4 there. But to rule out the possibility that someone is actually using the note I called for 7 GPUs (so the entire note) but with GPU id just assign the first 4 to GROMACS. I still get the same error. I also tried -gpu_id 00 or -gpu_id to change the CPU and to only use a single GPU but I always get: NOTE: You assigned GPUs to multiple MPI processes. --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Error on rank 1, will try to stop all ranks Halting parallel program gmx_mpi on CPU 1 out of 4 -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Mittwoch, 7. Januar 2015 14:13 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Max, On 07 Jan 2015, at 11:36, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi Carsten, thanks for your answer. I tried what you described and it is basically working except for letting multiple MPI workers use one GPU. In my setup I use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1. This is how I start GROMACS: mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s ../run1ns.tpr and I submit this using: qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu why are you using ppn=4? Shouldn't that be 8? Now I get the following errors (the output is longer but to keep it shorter I omitted the rest): Using 8 MPI processes Using 1 OpenMP thread per MPI process 7 GPUs detected on host ngpu-a4-06: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #6: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible 4 GPUs user-selected for this run. Mapping of GPUs to the 8 PP ranks in this node: #0, #0, #1, #1, #2, #2, #3, #3 NOTE: You assigned GPUs to multiple MPI processes. --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_too ls/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable Could it be that someone else's processes are running on that node while Gromacs tries to use the GPUs? Maybe try to the the whole node, maybe even in interactive mode to play around. Carsten For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Error on rank 1, will try to stop all ranks Halting parallel program gmx_mpi on CPU 1 out of 8 --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_too ls/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Error on rank 3, will try to stop all ranks Halting parallel program gmx_mpi on CPU 3 out of 8 -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Donnerstag, 18. Dezember 2014 17:27 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Max, On 18 Dec 2014, at 15:30, Ebert Maximilian m.eb...@umontreal.ca wrote: Dear list, I am benchmarking my system on a GPU cluster with 6 GPU's and two quad core CPUs for each node. First I am wondering if there is any output which confirms how many CPUs and GPUs were used during the run? I find the output
Re: [gmx-users] Working on a GPU cluster with GROMACS 5
I just thought we might add this information to the http://www.gromacs.org/Documentation/Acceleration_and_parallelization page. Could be useful for every user of a managed cluster. Usually you never come across this type of knowledge as a user. Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Ebert Maximilian Gesendet: Mittwoch, 7. Januar 2015 15:07 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Jiri, Yes this seems to be the problem. Thank you very much. The GPUs on this cluster are in the exclusive thread mode. I will ask the administrator if we can change this. Thank you very much! Max -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Jiri Kraus Gesendet: Mittwoch, 7. Januar 2015 14:58 An: gromacs.org_gmx-users@maillist.sys.kth.se Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Max, In which compute mode are the GPUs running? Do be able to share a GPU between multiple MPI ranks you either need to use the multi process service (MPS see: [1]) or let the GPUs run in default compute mode (see [2]). You can query the compute mode with nvidia-smi -q -d COMPUTE (see example output below) and change it with nvidia-smi -c DEFAULT. Changing the compute mode requires root. Hope this helps Jiri [1] https://docs.nvidia.com/deploy/pdf/CUDA_Multi_Process_Service_Overview.pdf [2] http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#compute-modes Example output of nvidia-smi -q -d COMPUTE: ==NVSMI LOG== Timestamp : Wed Jan 7 05:51:31 2015 Driver Version : 340.32 Attached GPUs : 6 GPU :04:00.0 Compute Mode: Default GPU :05:00.0 Compute Mode: Default GPU :08:00.0 Compute Mode: Default GPU :09:00.0 Compute Mode: Default GPU :83:00.0 Compute Mode: Default GPU :84:00.0 Compute Mode: Default Message: 5 Date: Wed, 7 Jan 2015 13:42:46 + From: Ebert Maximilian m.eb...@umontreal.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Message-ID: CAE65A26CFD123408751DCA75C2BA164255E0839@athens- cour.sim.umontreal.ca Content-Type: text/plain; charset=iso-8859-1 Hi Carsten, thanks again for your reply. The why our cluster is setup is that you ask for GPUs using the ppn command and not CPUs. Therefore, I put 4 there. But to rule out the possibility that someone is actually using the note I called for 7 GPUs (so the entire note) but with GPU id just assign the first 4 to GROMACS. I still get the same error. I also tried -gpu_id 00 or -gpu_id to change the CPU and to only use a single GPU but I always get: NOTE: You assigned GPUs to multiple MPI processes. --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs- 5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Error on rank 1, will try to stop all ranks Halting parallel program gmx_mpi on CPU 1 out of 4 -Urspr?ngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Mittwoch, 7. Januar 2015 14:13 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Max, On 07 Jan 2015, at 11:36, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi Carsten, thanks for your answer. I tried what you described and it is basically working except for letting multiple MPI workers use one GPU. In my setup I use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1. This is how I start GROMACS: mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s ../run1ns.tpr and I submit this using: qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu why are you using ppn=4? Shouldn't that be 8? Now I get the following errors (the output is longer but to keep it shorter I omitted the rest): Using 8 MPI processes Using 1 OpenMP thread per MPI process 7 GPUs detected on host ngpu-a4-06: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1
Re: [gmx-users] Working on a GPU cluster with GROMACS 5
Hi Carsten, thanks for your answer. I tried what you described and it is basically working except for letting multiple MPI workers use one GPU. In my setup I use 4 GPUs with 8 MPI workers and hence 8 CPUs and OpenMP 1. This is how I start GROMACS: mpirun -np 8 gmx_mpi mdrun -gpu_id 00112233 -v -x -deffnm run1ns -s ../run1ns.tpr and I submit this using: qsub -q @test -lnodes=1:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu Now I get the following errors (the output is longer but to keep it shorter I omitted the rest): Using 8 MPI processes Using 1 OpenMP thread per MPI process 7 GPUs detected on host ngpu-a4-06: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #6: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible 4 GPUs user-selected for this run. Mapping of GPUs to the 8 PP ranks in this node: #0, #0, #1, #1, #2, #2, #3, #3 NOTE: You assigned GPUs to multiple MPI processes. --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Error on rank 1, will try to stop all ranks Halting parallel program gmx_mpi on CPU 1 out of 8 --- Program gmx_mpi, VERSION 5.0.1 Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61 Fatal error: cudaMallocHost of size 4 bytes failed: all CUDA-capable devices are busy or unavailable For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Error on rank 3, will try to stop all ranks Halting parallel program gmx_mpi on CPU 3 out of 8 -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] Im Auftrag von Carsten Kutzner Gesendet: Donnerstag, 18. Dezember 2014 17:27 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] Working on a GPU cluster with GROMACS 5 Hi Max, On 18 Dec 2014, at 15:30, Ebert Maximilian m.eb...@umontreal.ca wrote: Dear list, I am benchmarking my system on a GPU cluster with 6 GPU's and two quad core CPUs for each node. First I am wondering if there is any output which confirms how many CPUs and GPUs were used during the run? I find the output for GPUs in the log file but only for a single node. When I use multiple nodes why don't the other nodes show up in the log file as hosts? For instance in this example I used two nodes and claimed 4 GPUs each but got this in my log file: 6 GPUs detected on host ngpu-a4-01: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible 4 GPUs auto-selected for this run. Mapping of GPUs to the 4 PP ranks in this node: #0, #1, #2, #3 This will be the same across all nodes. Gromacs will refuse to run if there are not enough GPUs on any of your other nodes. ngpu-a4-02 is not shown here. Any idea? The job was submitted in the following way: qsub -q @test -lnodes=2:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu and the gromacs_run_gpu file: #!/bin/csh # #PBS -o result_run10ns96-8.dat #PBS -j oe #PBS -W umask=022 #PBS -r n cd 8_gpu module add CUDA module load gromacs/5.0.1-gpu mpirun gmx_mpi mdrun -v -x -deffnm 10ns_rep1-8GPU Another question I had was how can I define the number of CPUs and check if they were really used? Use -ntomp to control how many OpenMP threads each of your MPI processes will have. This way you can make use of all cores you have on each node. I can't find any information about the number of CPUs in the log file. Look for Using . MPI processes Using . OpenMP threads per MPI process in the log file. I would also like to try combinations like 4
[gmx-users] Working on a GPU cluster with GROMACS 5
Dear list, I am benchmarking my system on a GPU cluster with 6 GPU’s and two quad core CPUs for each node. First I am wondering if there is any output which confirms how many CPUs and GPUs were used during the run? I find the output for GPUs in the log file but only for a single node. When I use multiple nodes why don’t the other nodes show up in the log file as hosts? For instance in this example I used two nodes and claimed 4 GPUs each but got this in my log file: 6 GPUs detected on host ngpu-a4-01: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #2: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #3: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #4: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #5: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible 4 GPUs auto-selected for this run. Mapping of GPUs to the 4 PP ranks in this node: #0, #1, #2, #3 ngpu-a4-02 is not shown here. Any idea? The job was submitted in the following way: qsub -q @test -lnodes=2:ppn=4 -lwalltime=1:00:00 gromacs_run_gpu and the gromacs_run_gpu file: #!/bin/csh # #PBS -o result_run10ns96-8.dat #PBS -j oe #PBS -W umask=022 #PBS -r n cd 8_gpu module add CUDA module load gromacs/5.0.1-gpu mpirun gmx_mpi mdrun -v -x -deffnm 10ns_rep1-8GPU Another question I had was how can I define the number of CPUs and check if they were really used? I can’t find any information about the number of CPUs in the log file. I would also like to try combinations like 4 CPUs + 1 GPU or 2 CPUs + 2 GPU. How do I set this up? Thank you very much for your help, Max -- 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] g_tune_pme_mpi is not compatible to mdrun_mpi
Hi, This all sounds super interesting. However, is there anything I can do for now or do I need to just find the best combination by hand? Thank you very much, Max -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten Kutzner Sent: Montag, 29. September 2014 19:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi On 29 Sep 2014, at 18:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, That seems suitable. Oh, it just occurred to me that on systems that use the Load Leveler, we have no means of specifying the number of MPI ranks on the command line, since 'poe' has no switch for that. So at least for this case I guess we also need to make the test optional. Carsten Mark On Mon, Sep 29, 2014 at 6:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, On 29 Sep 2014, at 18:17, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, It can't be fixed, because there is no surefire way to run an arbitrary tpr on arbitrary number of ranks, regardless of how you guess -npme might succeed. What about making this check on two ranks always, regardless of what was specified on the g_tune_pme command line? On two ranks, we will never have separate PME ranks, so it should always work, since we end up with two ranks, doing PP and then PME. If the system is so small that you can not decompose it in two DD domains, there is no use to do tuning anyway. So even if you say g_tune_pme -np 48 -s input.tpr we first check with mpirun -np 2 mdrun -s input.tpr and only after that continue with -np 48. Carsten We should just make the check optional, instead of being a deal breaker. Mark On Sep 29, 2014 4:35 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, I see where the problem is. There is an initial check in g_tune_pme to make sure that parallel runs can be executed at all. This is being run with the automatic number of PME-only ranks, which is 11 for your input file. Unfortunately, this results in 37 PP ranks, for which no domain decomposition can be found. At some point in the past we discussed that this could happen and it should be fixed. Will open a bug entry. Thanks, Carsten On 29 Sep 2014, at 15:36, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi, this ist he command: setenv MDRUN mdrun_mpi g_tune_pme_mpi -np 48 -s ../eq_nvt/1ZG4_nvt.tpr -launch Here the output of perf.out P E R F O R M A N C E R E S U L T S g_tune_pme_mpi for Gromacs VERSION 5.0.1 Number of ranks : 48 The mpirun command is : mpirun Passing # of ranks via : -np The mdrun command is : mdrun_mpi mdrun args benchmarks : -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g bench.log Benchmark steps : 1000 dlb equilibration steps : 100 mdrun args at launchtime: Repeats for each test : 2 Input file : ../eq_nvt/1ZG4_nvt.tpr PME/PP load estimate : 0.151964 Number of particles : 39489 Coulomb type : PME Grid spacing x y z : 0.114561 0.114561 0.114561 Van der Waals type : Cut-off Will try these real/reciprocal workload settings: No. scaling rcoulomb nkx nky nkz spacing rvdw tpr file 0 1.00 1.20 72 72 72 0.12 1.20 ../eq_nvt/1ZG4_nvt_bench00.tpr 1 1.10 1.32 64 64 64 0.132000 1.32 ../eq_nvt/1ZG4_nvt_bench01.tpr 2 1.20 1.44 60 60 60 0.144000 1.44 ../eq_nvt/1ZG4_nvt_bench02.tpr Note that in addition to the Coulomb radius and the Fourier grid other input settings were also changed (see table above). Please check if the modified settings are appropriate. Individual timings for input file 0 (../eq_nvt/1ZG4_nvt_bench00.tpr): PME ranks Gcycles ns/dayPME/fRemark Cannot run the benchmark simulations! Please check the error message of mdrun for the source of the problem. Did you provide a command line argument that neither g_tune_pme nor mdrun understands? Offending command: mpirun -np 48 mdrun_mpi -npme 11 -s ../eq_nvt/1ZG4_nvt_bench00.tpr -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g bench.log -nsteps 1 -quiet and here are parts of the bench.log: Log file opened on Mon Sep 29 08:56:38 2014 Host: node-e1-67 pid: 24470 rank ID: 0 number of ranks: 48 GROMACS:gmx mdrun, VERSION 5.0.1 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten
[gmx-users] AMBER FF naming and caps
Dear list, I am a little bit confused regarding the preparation needed to use the AMBER FF in GROMACS 5.0.1. I have a simple PDB file of a protein and I use this as input to pdb2gmx. I selected the AMBER FF during the creation process: gmx_mpi pdb2gmx -f protein.pdb -o protein_processed.gro -water spce This generates the gro, top and itp file. Now when I open the gro file in VMD I get an unusual bond between the last two residues of the protein chain. I already figured out why this is. The last amino acid has a charged carboxylate with the atom type OC1 and OC2 which are not identified as amino acids by VMD. After further reading of the manual I found this paragraph: The AMBER force fields have unique forms for the terminal residues, and these are incompatible with the -ter mechanism. You need to prefix your N- or C-terminal residue names with N or C respectively to use these forms, making sure you preserve the format of the coordinate file. Alternatively, use named terminating residues (e.g. ACE, NME). Now I was thinking that I have to change the name of the N and C terminal residue. However, looking into my top file GROMACS already knows about AMBER's naming convention: ... ; residue 290 TRP rtp CTRP q -1.0 4049 N290TRP N 4049-0.3821 14.01 ; qtot -6.382 4050 H290TRP H 4050 0.2681 1.008 ; qtot -6.114 4051 CT290TRP CA 4051-0.2084 12.01 ; qtot -6.322 ... Now my question do I have to do anything or is GROMACS 5 taking care of the correct termini in the AMBERE FF? Thank you very much, Max -- 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] AMBER FF naming and caps
Thank you very much for your help. This answered my questions. I wish you a great day, Max -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Montag, 29. September 2014 14:27 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] AMBER FF naming and caps On 9/29/14 5:58 AM, Ebert Maximilian wrote: Dear list, I am a little bit confused regarding the preparation needed to use the AMBER FF in GROMACS 5.0.1. I have a simple PDB file of a protein and I use this as input to pdb2gmx. I selected the AMBER FF during the creation process: gmx_mpi pdb2gmx -f protein.pdb -o protein_processed.gro -water spce This generates the gro, top and itp file. Now when I open the gro file in VMD I get an unusual bond between the last two residues of the protein chain. I already figured out why this is. The last amino acid has a charged carboxylate with the atom type OC1 and OC2 which are not identified as amino acids by VMD. After further reading of the manual I found this paragraph: The AMBER force fields have unique forms for the terminal residues, and these are incompatible with the -ter mechanism. You need to prefix your N- or C-terminal residue names with N or C respectively to use these forms, making sure you preserve the format of the coordinate file. Alternatively, use named terminating residues (e.g. ACE, NME). Now I was thinking that I have to change the name of the N and C terminal residue. However, looking into my top file GROMACS already knows about AMBER's naming convention: ... ; residue 290 TRP rtp CTRP q -1.0 4049 N290TRP N 4049-0.3821 14.01 ; qtot -6.382 4050 H290TRP H 4050 0.2681 1.008 ; qtot -6.114 4051 CT290TRP CA 4051-0.2084 12.01 ; qtot -6.322 ... Now my question do I have to do anything or is GROMACS 5 taking care of the correct termini in the AMBERE FF? The information about manual prefixing is outdated, so we'll need to clean that up. Bonds drawn in VMD are not definitive, but those in the topology are. If you have multiple chains and the bonded structure in the topology is correct, then there's no problem. -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 jalem...@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-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] g_tune_pme_mpi is not compatible to mdrun_mpi
Dear list, I tried using g_tune_pme_mpi with the command: mpirun -np 24 g_tune_pme_mpi -np 24 -s 1ZG4_nvt.tpr -launch on GROMACS 5.0.1 but I get the following error message: -- mpirun was unable to launch the specified application as it could not find an executable: Executable: mdrun Node: while attempting to start process rank 0. -- 24 total processes failed to start Any idea why this is? Shouldn't g_tune_pme_mpi call mdrun_mpi instead? Thank you very much, Max -- 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.
