Re: [gmx-users] Help for gmx enemat
Hi Justin, You are right!! Thanks a lot!! Your help was precious. Again thanks. Valerio 2016-01-14 18:26 GMT+01:00 Justin Lemkul : > > > On 1/14/16 12:18 PM, valerio di giulio wrote: > >> Hi Justin, >> >> I need the LJ potential just between the two DNAs, instead gmx energy >> calculates the total LJ energy. Is it right? >> >> > gmx energy does what you tell it. You specified DNA1 and DNA2 as > energygrps, therefore all short-range nonbonded interaction energies are > decomposed. This is actually no different than what you were trying to do > with gmx enemat, except that enemat is a more roundabout way to obtain what > you want. The information you need is in the .edr file; gmx energy is the > first port of call for extracting anything related to energy. > > -Justin > > Valerio >> >> Il giovedì 14 gennaio 2016, Justin Lemkul > > ha scritto: >> >> >> >>> >>> On 1/14/16 4:48 AM, Peter Stern wrote: >>> >>> Hi Valerio, >>>> >>>> Sorry, I don't know then. >>>> >>>> Peter >>>> >>>> -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 valerio >>>> di giulio >>>> Sent: Wednesday, January 13, 2016 11:17 PM >>>> To: gmx-us...@gromacs.org >>>> Subject: Re: [gmx-users] Help for gmx enemat >>>> >>>> Hi Peter, >>>> >>>> I have already created an index file with make_ndx in which I specify >>>> what atoms are in DNA1 and DNA2 groups. Moreover the two groups are >>>> present >>>> in the file topol.top. Indeed GROMACS doesn't produce any error about >>>> the >>>> declaration of them in the file .mdp. I send you also my topol.top file >>>> for >>>> clarity: >>>> >>>> >>> You don't need g_enemat to get the numbers you want. Just use g_energy; >>> there's no point in plotting them as a matrix when all you need are the >>> values. >>> >>> -Justin >>> >>> . >>> >>>> >>>> ; GROMACS topology >>>> ; >>>> ; Include the force field >>>> #include "/amber03.ff/forcefield.itp" >>>> >>>> ; Include chain topologies >>>> #include "topol1.itp" >>>> #include "topol2.itp" >>>> >>>> ; Include water topology >>>> #include "amber03.ff/tip4p.itp" >>>> >>>> ; Include generic ion topology >>>> #include "amber03.ff/ions.itp" >>>> >>>> [ system ] >>>> Two all-AT in water >>>> >>>> [ molecules ] >>>> DNA11 >>>> DNA21 >>>> SOL 39390 >>>> NA 190 >>>> CL 146 >>>> >>>> . >>>> >>>> Thanks, >>>> >>>> Valerio >>>> >>>> 2016-01-13 20:40 GMT+01:00 Peter Stern : >>>> >>>> I believe that you need to define which nucleotides are in each group >>>> >>>>> DNA1 and DNA2 using make_ndx, since those are not "default" groups. I >>>>> think that you can do this and then do an Metin -rerun just to define >>>>> the new groups. >>>>> >>>>> Peter >>>>> >>>>> Sent from my iPad >>>>> >>>>> On 13 בינו׳ 2016, at 20:53, valerio di giulio >>>>> >>>>>> >>>>>> >>>>>> wrote: >>>>> >>>>> >>>>>> Hi, >>>>>> >>>>>> I have a problem with the use of "gmx enemat". I'm trying to >>>>>> calculate the contribution of SH-LJ to the potential that exists >>>>>> between two DNA strands with GROMACS 5.1.1. I've already got a >>>>>> Potential of Mean Force doing an umbrella sampling. >>>>>> For this reason I have already many files .edr each one linked to a >>>>>> >>>>>> window, >>>>> >>>>> from >>>>>> which I would like to extract the SH-LJ contribution but every time >>>>>
Re: [gmx-users] Help for gmx enemat
On 1/14/16 12:18 PM, valerio di giulio wrote: Hi Justin, I need the LJ potential just between the two DNAs, instead gmx energy calculates the total LJ energy. Is it right? gmx energy does what you tell it. You specified DNA1 and DNA2 as energygrps, therefore all short-range nonbonded interaction energies are decomposed. This is actually no different than what you were trying to do with gmx enemat, except that enemat is a more roundabout way to obtain what you want. The information you need is in the .edr file; gmx energy is the first port of call for extracting anything related to energy. -Justin Valerio Il giovedì 14 gennaio 2016, Justin Lemkul > ha scritto: On 1/14/16 4:48 AM, Peter Stern wrote: Hi Valerio, Sorry, I don't know then. Peter -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 valerio di giulio Sent: Wednesday, January 13, 2016 11:17 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Help for gmx enemat Hi Peter, I have already created an index file with make_ndx in which I specify what atoms are in DNA1 and DNA2 groups. Moreover the two groups are present in the file topol.top. Indeed GROMACS doesn't produce any error about the declaration of them in the file .mdp. I send you also my topol.top file for clarity: You don't need g_enemat to get the numbers you want. Just use g_energy; there's no point in plotting them as a matrix when all you need are the values. -Justin . ; GROMACS topology ; ; Include the force field #include "/amber03.ff/forcefield.itp" ; Include chain topologies #include "topol1.itp" #include "topol2.itp" ; Include water topology #include "amber03.ff/tip4p.itp" ; Include generic ion topology #include "amber03.ff/ions.itp" [ system ] Two all-AT in water [ molecules ] DNA11 DNA21 SOL 39390 NA 190 CL 146 . Thanks, Valerio 2016-01-13 20:40 GMT+01:00 Peter Stern : I believe that you need to define which nucleotides are in each group DNA1 and DNA2 using make_ndx, since those are not "default" groups. I think that you can do this and then do an Metin -rerun just to define the new groups. Peter Sent from my iPad On 13 בינו׳ 2016, at 20:53, valerio di giulio wrote: Hi, I have a problem with the use of "gmx enemat". I'm trying to calculate the contribution of SH-LJ to the potential that exists between two DNA strands with GROMACS 5.1.1. I've already got a Potential of Mean Force doing an umbrella sampling. For this reason I have already many files .edr each one linked to a window, from which I would like to extract the SH-LJ contribution but every time I use "enemat" this is the output: .. GROMACS: gmx enemat, VERSION 5.1.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx enemat umbrella1e.edr -ljsr Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file Will select half-matrix of energies with 0 elements Last energy frame read 500 time 500.000 Will build energy half-matrix of 2 groups, 0 elements, over 501 frames Segmentation fault (core dumped) ... Although I have written to the .mdp file: energygrps = DNA1 DNA2 Thank you in advance, Valerio Di Giulio -- 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 r
[gmx-users] Help for gmx enemat
Hi Justin, I need the LJ potential just between the two DNAs, instead gmx energy calculates the total LJ energy. Is it right? Valerio Il giovedì 14 gennaio 2016, Justin Lemkul > ha scritto: > > > On 1/14/16 4:48 AM, Peter Stern wrote: > >> Hi Valerio, >> >> Sorry, I don't know then. >> >> Peter >> >> -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 valerio >> di giulio >> Sent: Wednesday, January 13, 2016 11:17 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Help for gmx enemat >> >> Hi Peter, >> >> I have already created an index file with make_ndx in which I specify >> what atoms are in DNA1 and DNA2 groups. Moreover the two groups are present >> in the file topol.top. Indeed GROMACS doesn't produce any error about the >> declaration of them in the file .mdp. I send you also my topol.top file for >> clarity: >> > > You don't need g_enemat to get the numbers you want. Just use g_energy; > there's no point in plotting them as a matrix when all you need are the > values. > > -Justin > > . >> >> ; GROMACS topology >> ; >> ; Include the force field >> #include "/amber03.ff/forcefield.itp" >> >> ; Include chain topologies >> #include "topol1.itp" >> #include "topol2.itp" >> >> ; Include water topology >> #include "amber03.ff/tip4p.itp" >> >> ; Include generic ion topology >> #include "amber03.ff/ions.itp" >> >> [ system ] >> Two all-AT in water >> >> [ molecules ] >> DNA11 >> DNA21 >> SOL 39390 >> NA 190 >> CL 146 >> >> . >> >> Thanks, >> >> Valerio >> >> 2016-01-13 20:40 GMT+01:00 Peter Stern : >> >> I believe that you need to define which nucleotides are in each group >>> DNA1 and DNA2 using make_ndx, since those are not "default" groups. I >>> think that you can do this and then do an Metin -rerun just to define >>> the new groups. >>> >>> Peter >>> >>> Sent from my iPad >>> >>> On 13 בינו׳ 2016, at 20:53, valerio di giulio >>>> >>>> >>> wrote: >>> >>>> >>>> Hi, >>>> >>>> I have a problem with the use of "gmx enemat". I'm trying to >>>> calculate the contribution of SH-LJ to the potential that exists >>>> between two DNA strands with GROMACS 5.1.1. I've already got a >>>> Potential of Mean Force doing an umbrella sampling. >>>> For this reason I have already many files .edr each one linked to a >>>> >>> window, >>> >>>> from >>>> which I would like to extract the SH-LJ contribution but every time >>>> I use "enemat" this is the output: >>>> >>>> .. >>>> >>>> GROMACS: gmx enemat, VERSION 5.1.1 >>>> Executable: /usr/local/gromacs/bin/gmx >>>> Data prefix: /usr/local/gromacs >>>> Command line: >>>> gmx enemat umbrella1e.edr -ljsr >>>> >>>> Opened ener.edr as single precision energy file Will read groupnames >>>> from inputfile Read 2 groups group 0WARNING! could not find group >>>> Coul-SR:DNA1-DNA1 (0,0)in energy >>>> >>> file >>> >>>> WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file >>>> WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file >>>> WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file >>>> group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in >>>> energy >>>> >>> file >>> >>>> WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file >>>> >>>> Will select half-matrix of energies with 0 elements Last energy >>>> frame read 500 time 500.000 Will build energy half-matrix of 2 >>>> groups, 0 elements, over 501 frames Segmentation fault (core dumped) >>>> >>>> ... >>>> >>>> Although I have written to the .mdp file: >>>> >>>> energygrps = DNA1 DNA2 >>>> >>>>
Re: [gmx-users] Help for gmx enemat
On 1/14/16 4:48 AM, Peter Stern wrote: Hi Valerio, Sorry, I don't know then. Peter -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 valerio di giulio Sent: Wednesday, January 13, 2016 11:17 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Help for gmx enemat Hi Peter, I have already created an index file with make_ndx in which I specify what atoms are in DNA1 and DNA2 groups. Moreover the two groups are present in the file topol.top. Indeed GROMACS doesn't produce any error about the declaration of them in the file .mdp. I send you also my topol.top file for clarity: You don't need g_enemat to get the numbers you want. Just use g_energy; there's no point in plotting them as a matrix when all you need are the values. -Justin . ; GROMACS topology ; ; Include the force field #include "/amber03.ff/forcefield.itp" ; Include chain topologies #include "topol1.itp" #include "topol2.itp" ; Include water topology #include "amber03.ff/tip4p.itp" ; Include generic ion topology #include "amber03.ff/ions.itp" [ system ] Two all-AT in water [ molecules ] DNA11 DNA21 SOL 39390 NA 190 CL 146 . Thanks, Valerio 2016-01-13 20:40 GMT+01:00 Peter Stern : I believe that you need to define which nucleotides are in each group DNA1 and DNA2 using make_ndx, since those are not "default" groups. I think that you can do this and then do an Metin -rerun just to define the new groups. Peter Sent from my iPad On 13 בינו׳ 2016, at 20:53, valerio di giulio wrote: Hi, I have a problem with the use of "gmx enemat". I'm trying to calculate the contribution of SH-LJ to the potential that exists between two DNA strands with GROMACS 5.1.1. I've already got a Potential of Mean Force doing an umbrella sampling. For this reason I have already many files .edr each one linked to a window, from which I would like to extract the SH-LJ contribution but every time I use "enemat" this is the output: .. GROMACS: gmx enemat, VERSION 5.1.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx enemat umbrella1e.edr -ljsr Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file Will select half-matrix of energies with 0 elements Last energy frame read 500 time 500.000 Will build energy half-matrix of 2 groups, 0 elements, over 501 frames Segmentation fault (core dumped) ... Although I have written to the .mdp file: energygrps = DNA1 DNA2 Thank you in advance, Valerio Di Giulio -- 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. -- == 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?
Re: [gmx-users] Help for gmx enemat
Hi Valerio, Sorry, I don't know then. Peter -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 valerio di giulio Sent: Wednesday, January 13, 2016 11:17 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Help for gmx enemat Hi Peter, I have already created an index file with make_ndx in which I specify what atoms are in DNA1 and DNA2 groups. Moreover the two groups are present in the file topol.top. Indeed GROMACS doesn't produce any error about the declaration of them in the file .mdp. I send you also my topol.top file for clarity: . ; GROMACS topology ; ; Include the force field #include "/amber03.ff/forcefield.itp" ; Include chain topologies #include "topol1.itp" #include "topol2.itp" ; Include water topology #include "amber03.ff/tip4p.itp" ; Include generic ion topology #include "amber03.ff/ions.itp" [ system ] Two all-AT in water [ molecules ] DNA11 DNA21 SOL 39390 NA 190 CL 146 . Thanks, Valerio 2016-01-13 20:40 GMT+01:00 Peter Stern : > I believe that you need to define which nucleotides are in each group > DNA1 and DNA2 using make_ndx, since those are not "default" groups. I > think that you can do this and then do an Metin -rerun just to define > the new groups. > > Peter > > Sent from my iPad > > > On 13 בינו׳ 2016, at 20:53, valerio di giulio > > > wrote: > > > > Hi, > > > > I have a problem with the use of "gmx enemat". I'm trying to > > calculate the contribution of SH-LJ to the potential that exists > > between two DNA strands with GROMACS 5.1.1. I've already got a > > Potential of Mean Force doing an umbrella sampling. > > For this reason I have already many files .edr each one linked to a > window, > > from > > which I would like to extract the SH-LJ contribution but every time > > I use "enemat" this is the output: > > > > .. > > > > GROMACS: gmx enemat, VERSION 5.1.1 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Command line: > > gmx enemat umbrella1e.edr -ljsr > > > > Opened ener.edr as single precision energy file Will read groupnames > > from inputfile Read 2 groups group 0WARNING! could not find group > > Coul-SR:DNA1-DNA1 (0,0)in energy > file > > WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file > > WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file > > WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file > > group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in > > energy > file > > WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file > > > > Will select half-matrix of energies with 0 elements Last energy > > frame read 500 time 500.000 Will build energy half-matrix of 2 > > groups, 0 elements, over 501 frames Segmentation fault (core dumped) > > > > ... > > > > Although I have written to the .mdp file: > > > > energygrps = DNA1 DNA2 > > > > Thank you in advance, > > > > Valerio Di Giulio > > -- > > 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] Help for gmx enemat
Hi Peter, I have already created an index file with make_ndx in which I specify what atoms are in DNA1 and DNA2 groups. Moreover the two groups are present in the file topol.top. Indeed GROMACS doesn't produce any error about the declaration of them in the file .mdp. I send you also my topol.top file for clarity: . ; GROMACS topology ; ; Include the force field #include "/amber03.ff/forcefield.itp" ; Include chain topologies #include "topol1.itp" #include "topol2.itp" ; Include water topology #include "amber03.ff/tip4p.itp" ; Include generic ion topology #include "amber03.ff/ions.itp" [ system ] Two all-AT in water [ molecules ] DNA11 DNA21 SOL 39390 NA 190 CL 146 . Thanks, Valerio 2016-01-13 20:40 GMT+01:00 Peter Stern : > I believe that you need to define which nucleotides are in each group DNA1 > and DNA2 using make_ndx, since those are not "default" groups. I think > that you can do this and then do an Metin -rerun just to define the new > groups. > > Peter > > Sent from my iPad > > > On 13 בינו׳ 2016, at 20:53, valerio di giulio > wrote: > > > > Hi, > > > > I have a problem with the use of "gmx enemat". I'm trying to calculate > > the contribution of SH-LJ to the potential that exists between two DNA > > strands with GROMACS 5.1.1. I've already got a Potential of Mean Force > > doing an umbrella sampling. > > For this reason I have already many files .edr each one linked to a > window, > > from > > which I would like to extract the SH-LJ contribution but every time I use > > "enemat" this is the output: > > > > .. > > > > GROMACS: gmx enemat, VERSION 5.1.1 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Command line: > > gmx enemat umbrella1e.edr -ljsr > > > > Opened ener.edr as single precision energy file > > Will read groupnames from inputfile > > Read 2 groups > > group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy > file > > WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file > > WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file > > WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file > > group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy > file > > WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file > > > > Will select half-matrix of energies with 0 elements > > Last energy frame read 500 time 500.000 > > Will build energy half-matrix of 2 groups, 0 elements, over 501 frames > > Segmentation fault (core dumped) > > > > ... > > > > Although I have written to the .mdp file: > > > > energygrps = DNA1 DNA2 > > > > Thank you in advance, > > > > Valerio Di Giulio > > -- > > 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] Help for gmx enemat
I believe that you need to define which nucleotides are in each group DNA1 and DNA2 using make_ndx, since those are not "default" groups. I think that you can do this and then do an Metin -rerun just to define the new groups. Peter Sent from my iPad > On 13 בינו׳ 2016, at 20:53, valerio di giulio > wrote: > > Hi, > > I have a problem with the use of "gmx enemat". I'm trying to calculate > the contribution of SH-LJ to the potential that exists between two DNA > strands with GROMACS 5.1.1. I've already got a Potential of Mean Force > doing an umbrella sampling. > For this reason I have already many files .edr each one linked to a window, > from > which I would like to extract the SH-LJ contribution but every time I use > "enemat" this is the output: > > .. > > GROMACS: gmx enemat, VERSION 5.1.1 > Executable: /usr/local/gromacs/bin/gmx > Data prefix: /usr/local/gromacs > Command line: > gmx enemat umbrella1e.edr -ljsr > > Opened ener.edr as single precision energy file > Will read groupnames from inputfile > Read 2 groups > group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file > WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file > WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file > WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file > group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file > WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file > > Will select half-matrix of energies with 0 elements > Last energy frame read 500 time 500.000 > Will build energy half-matrix of 2 groups, 0 elements, over 501 frames > Segmentation fault (core dumped) > > ... > > Although I have written to the .mdp file: > > energygrps = DNA1 DNA2 > > Thank you in advance, > > Valerio Di Giulio > -- > 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] Help for gmx enemat
Hi, I have a problem with the use of "gmx enemat". I'm trying to calculate the contribution of SH-LJ to the potential that exists between two DNA strands with GROMACS 5.1.1. I've already got a Potential of Mean Force doing an umbrella sampling. For this reason I have already many files .edr each one linked to a window, from which I would like to extract the SH-LJ contribution but every time I use "enemat" this is the output: .. GROMACS: gmx enemat, VERSION 5.1.1 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx enemat umbrella1e.edr -ljsr Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file Will select half-matrix of energies with 0 elements Last energy frame read 500 time 500.000 Will build energy half-matrix of 2 groups, 0 elements, over 501 frames Segmentation fault (core dumped) ... Although I have written to the .mdp file: energygrps = DNA1 DNA2 Thank you in advance, Valerio Di Giulio -- 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.
