Re: [gmx-users] Tabulated potentials
Hi, On Tue, Feb 18, 2020 at 12:12 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > So I am using Iterative Boltzmann Inversion to get the CG potentials for a > cellobiose-water solution. During the first step of the simulation by > gromacs, I get the error, which I think it might be due to some large > forces, causing the distance between the CG beads to increase to values > more than the length of the table. The bonded tables have values in > between 0 to 0.5 nm for r. > As far as I recall the error messages that you got was something like "A tabulated bond interaction table number 4 is out of the table range: r 0.575410, between table indices 575 and 576, table length 501" Your table is up to the 0.5 (501 lines), but the program is looking for a values of 0.575410 nm, that it is out of the range of the values for your table. Could it be that one of cellobiose-water distances is 0.575410 nm in the first frames? The errors seems to indicate that you need a longer table at least up 0.58 nm or more (even if it corresponds to high potential values). Note that if your table is for non-bonded interactions, then also the mdp parameters set requirement on the table lengths (see http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=table#tables ) Best regards Alessandra > My best, > Ali > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: maandag 17 februari 2020 9:34 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < > ali.khoday...@student.kuleuven.be> wrote: > > > Thank you Alessandra. However, fixing the topology did not remove the > > error. It still stands as before: > > > > A tabulated bond interaction table number 4 is out of the table range: > > r 0.575410, between table indices 575 and 576, table length 501 > > > > > Where exactly did you get this error? > > It looks like that your table is not covering all the request values (that > means that it is too short) or the file is missing same values. > > Best regards > Alessandra > > > > > Anyone has any idea why it could be happening? > > > > My best, > > Ali > > > > > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > > Alessandra Villa > > Sent: donderdag 13 februari 2020 16:28 > > To: gmx-us...@gromacs.org; gromacs.org_gmx-users < > > gromacs.org_gmx-users@maillist.sys.kth.se> > > Subject: Re: [gmx-users] Tabulated potentials > > > > Hi, > > > > On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < > > ali.khoday...@student.kuleuven.be> wrote: > > > > > Dear Gromacs users, > > > > > > I’ve got a question regarding the tabulated potentials for bonded > > > interactions. > > > > > > Gromacs recognises and reads the non-bonded potential tables through > > > the energy groups specified. But how can I refer each bond type to > > > its > > table? > > > > > > I have derived coarse-grained potentials for a cellobiose-water system. > > > There are 11 beads (4 bead types) in each cellobiose molecule, and > > > each water molecule is coarse-grained as one bead. Overall, there > > > are > > > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > > > types, and 2 dihedral potential tables for two types of dihedrals. > > > The tables are named as table_b1.xvg, table_b2.xvg, and so on. > > > > > Now my question is, how does gromacs recognise which table is > > regarding > > > which bonded term? The simulation crashes at the very beginning > > > giving me the following error: > > > > > > > > In topol.top one specifies which table is used for which interaction > > (bond, angle, dihedral). See the table below for the synthases > > > > > > http://manual.gromacs.org/documentation/current/reference-manual/topol > > ogies/topology-file-formats.html#topology-file > > > > Best regards > > Alessandra > > > > > > > > > A tabulated bond interaction table number 1 is out of the table range: > > > r 0.511823, between table indices 511 and 512, table length 501 > > > > > > I believe this is caused due to high forces on atoms indeed, but it > > > might be also beca
Re: [gmx-users] Tabulated potentials
So I am using Iterative Boltzmann Inversion to get the CG potentials for a cellobiose-water solution. During the first step of the simulation by gromacs, I get the error, which I think it might be due to some large forces, causing the distance between the CG beads to increase to values more than the length of the table. The bonded tables have values in between 0 to 0.5 nm for r. My best, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Alessandra Villa Sent: maandag 17 februari 2020 9:34 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Tabulated potentials Hi, On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Thank you Alessandra. However, fixing the topology did not remove the > error. It still stands as before: > > A tabulated bond interaction table number 4 is out of the table range: > r 0.575410, between table indices 575 and 576, table length 501 > > Where exactly did you get this error? It looks like that your table is not covering all the request values (that means that it is too short) or the file is missing same values. Best regards Alessandra > Anyone has any idea why it could be happening? > > My best, > Ali > > > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: donderdag 13 februari 2020 16:28 > To: gmx-us...@gromacs.org; gromacs.org_gmx-users < > gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > > On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < > ali.khoday...@student.kuleuven.be> wrote: > > > Dear Gromacs users, > > > > I’ve got a question regarding the tabulated potentials for bonded > > interactions. > > > > Gromacs recognises and reads the non-bonded potential tables through > > the energy groups specified. But how can I refer each bond type to > > its > table? > > > > I have derived coarse-grained potentials for a cellobiose-water system. > > There are 11 beads (4 bead types) in each cellobiose molecule, and > > each water molecule is coarse-grained as one bead. Overall, there > > are > > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > > types, and 2 dihedral potential tables for two types of dihedrals. > > The tables are named as table_b1.xvg, table_b2.xvg, and so on. > > > Now my question is, how does gromacs recognise which table is > regarding > > which bonded term? The simulation crashes at the very beginning > > giving me the following error: > > > > > In topol.top one specifies which table is used for which interaction > (bond, angle, dihedral). See the table below for the synthases > > > http://manual.gromacs.org/documentation/current/reference-manual/topol > ogies/topology-file-formats.html#topology-file > > Best regards > Alessandra > > > > > A tabulated bond interaction table number 1 is out of the table range: > > r 0.511823, between table indices 511 and 512, table length 501 > > > > I believe this is caused due to high forces on atoms indeed, but it > > might be also because tables are not specified to the correct bond type. > > > > > > Kind regards, > > Ali > > -- > > 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:
Re: [gmx-users] Tabulated potentials
Hi, On Fri, Feb 14, 2020 at 5:17 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Thank you Alessandra. However, fixing the topology did not remove the > error. It still stands as before: > > A tabulated bond interaction table number 4 is out of the table range: r > 0.575410, between table indices 575 and 576, table length 501 > > Where exactly did you get this error? It looks like that your table is not covering all the request values (that means that it is too short) or the file is missing same values. Best regards Alessandra > Anyone has any idea why it could be happening? > > My best, > Ali > > > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of > Alessandra Villa > Sent: donderdag 13 februari 2020 16:28 > To: gmx-us...@gromacs.org; gromacs.org_gmx-users < > gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] Tabulated potentials > > Hi, > > On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < > ali.khoday...@student.kuleuven.be> wrote: > > > Dear Gromacs users, > > > > I’ve got a question regarding the tabulated potentials for bonded > > interactions. > > > > Gromacs recognises and reads the non-bonded potential tables through > > the energy groups specified. But how can I refer each bond type to its > table? > > > > I have derived coarse-grained potentials for a cellobiose-water system. > > There are 11 beads (4 bead types) in each cellobiose molecule, and > > each water molecule is coarse-grained as one bead. Overall, there are > > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > > types, and 2 dihedral potential tables for two types of dihedrals. The > > tables are named as table_b1.xvg, table_b2.xvg, and so on. > > > Now my question is, how does gromacs recognise which table is regarding > > which bonded term? The simulation crashes at the very beginning giving > > me the following error: > > > > > In topol.top one specifies which table is used for which interaction > (bond, angle, dihedral). See the table below for the synthases > > > http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file > > Best regards > Alessandra > > > > > A tabulated bond interaction table number 1 is out of the table range: > > r 0.511823, between table indices 511 and 512, table length 501 > > > > I believe this is caused due to high forces on atoms indeed, but it > > might be also because tables are not specified to the correct bond type. > > > > > > Kind regards, > > Ali > > -- > > 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] Tabulated potentials
Thank you Alessandra. However, fixing the topology did not remove the error. It still stands as before: A tabulated bond interaction table number 4 is out of the table range: r 0.575410, between table indices 575 and 576, table length 501 Anyone has any idea why it could be happening? My best, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Alessandra Villa Sent: donderdag 13 februari 2020 16:28 To: gmx-us...@gromacs.org; gromacs.org_gmx-users Subject: Re: [gmx-users] Tabulated potentials Hi, On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Dear Gromacs users, > > I’ve got a question regarding the tabulated potentials for bonded > interactions. > > Gromacs recognises and reads the non-bonded potential tables through > the energy groups specified. But how can I refer each bond type to its table? > > I have derived coarse-grained potentials for a cellobiose-water system. > There are 11 beads (4 bead types) in each cellobiose molecule, and > each water molecule is coarse-grained as one bead. Overall, there are > 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle > types, and 2 dihedral potential tables for two types of dihedrals. The > tables are named as table_b1.xvg, table_b2.xvg, and so on. > Now my question is, how does gromacs recognise which table is regarding > which bonded term? The simulation crashes at the very beginning giving > me the following error: > > In topol.top one specifies which table is used for which interaction (bond, angle, dihedral). See the table below for the synthases http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file Best regards Alessandra > A tabulated bond interaction table number 1 is out of the table range: > r 0.511823, between table indices 511 and 512, table length 501 > > I believe this is caused due to high forces on atoms indeed, but it > might be also because tables are not specified to the correct bond type. > > > Kind regards, > Ali > -- > 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] Tabulated potentials
Hi, On Wed, Feb 12, 2020 at 10:59 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Dear Gromacs users, > > I’ve got a question regarding the tabulated potentials for bonded > interactions. > > Gromacs recognises and reads the non-bonded potential tables through the > energy groups specified. But how can I refer each bond type to its table? > > I have derived coarse-grained potentials for a cellobiose-water system. > There are 11 beads (4 bead types) in each cellobiose molecule, and each > water molecule is coarse-grained as one bead. Overall, there are 3 bonded > terms for 3 bond types, 3 anglular potentials for 3 angle types, and 2 > dihedral potential tables for two types of dihedrals. The tables are named > as table_b1.xvg, table_b2.xvg, and so on. > Now my question is, how does gromacs recognise which table is regarding > which bonded term? The simulation crashes at the very beginning giving me > the following error: > > In topol.top one specifies which table is used for which interaction (bond, angle, dihedral). See the table below for the synthases http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file Best regards Alessandra > A tabulated bond interaction table number 1 is out of the table range: r > 0.511823, between table indices 511 and 512, table length 501 > > I believe this is caused due to high forces on atoms indeed, but it might > be also because tables are not specified to the correct bond type. > > > Kind regards, > Ali > -- > 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] Tabulated potentials
Dear Gromacs users, I’ve got a question regarding the tabulated potentials for bonded interactions. Gromacs recognises and reads the non-bonded potential tables through the energy groups specified. But how can I refer each bond type to its table? I have derived coarse-grained potentials for a cellobiose-water system. There are 11 beads (4 bead types) in each cellobiose molecule, and each water molecule is coarse-grained as one bead. Overall, there are 3 bonded terms for 3 bond types, 3 anglular potentials for 3 angle types, and 2 dihedral potential tables for two types of dihedrals. The tables are named as table_b1.xvg, table_b2.xvg, and so on. Now my question is, how does gromacs recognise which table is regarding which bonded term? The simulation crashes at the very beginning giving me the following error: A tabulated bond interaction table number 1 is out of the table range: r 0.511823, between table indices 511 and 512, table length 501 I believe this is caused due to high forces on atoms indeed, but it might be also because tables are not specified to the correct bond type. Kind regards, Ali -- 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] Tabulated potentials
Hi, OK that's a good start. Check also at long range, and consider using the dispersion correction (iirc maybe it does some numerical integration of the table?), or maybe really long cutoffs. Assuming your wrong-pressure result is reproducible from different starting velocities, then it could also be a property of the model, which you should investigate by looking also at other properties, others' work, etc. Mark On Mon, May 25, 2015 at 10:15 AM 张正财 zhangzhe...@mail.iggcas.ac.cn wrote: Dear Mark， I used mdrun -rerun. My table reproduced the potential and force. Best, Zhengcai Date: Sat, 23 May 2015 11:55:22 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Tabulated potentials Message-ID: camnumatlq-88bmycdyoiysoz72smag6uptyzcjxuasb5_8e...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Does your table reproduce the potential and force for two methane atoms at different distances (use mdrun -rerun) Mark On Sat, May 23, 2015 at 1:21 PM ??? zhangzhe...@mail.iggcas.ac.cn wrote: Dear all, I want to add the Morse potential ( U=D*[exp(a*(1-r/r0)-2*exp(a/2*(1-r/r0)] ) for nonbonded interactions between CH4-CH4. So, I made three table files to correspond to the interactions between H-H, C-H, and C-C, and I changed vdwtype=user ,Dispcorr=no , energrps = C H , and energrps_table = C C C H H H. However, when I used NVT ensemble to calculate the pressure of pure methane system, I didnot get accurate pressure, actually the pressure is about 20 MPa smaller than the experiment value. Could you give me some suggestions about what is wrong with my set or what I missed in adding the table? Sincerely yours, Zhengcai, -- Gromacs Users mailing list * Please search the archive at *http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List* http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read *http://www.gromacs.org/Support/Mailing_Lists* http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit *https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users* https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Message: 4 Date: Sat, 23 May 2015 11:55:22 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Tabulated potentials Message-ID: camnumatlq-88bmycdyoiysoz72smag6uptyzcjxuasb5_8e...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 -- 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] Tabulated potentials
Hi, Does your table reproduce the potential and force for two methane atoms at different distances (use mdrun -rerun) Mark On Sat, May 23, 2015 at 1:21 PM 张正财 zhangzhe...@mail.iggcas.ac.cn wrote: Dear all, I want to add the Morse potential ( U=D*[exp(a*(1-r/r0)-2*exp(a/2*(1-r/r0)] ) for nonbonded interactions between CH4-CH4. So, I made three table files to correspond to the interactions between H-H, C-H, and C-C, and I changed vdwtype=user ,Dispcorr=no , energrps = C H , and energrps_table = C C C H H H. However, when I used NVT ensemble to calculate the pressure of pure methane system, I didnot get accurate pressure, actually the pressure is about 20 MPa smaller than the experiment value. Could you give me some suggestions about what is wrong with my set or what I missed in adding the table? Sincerely yours, Zhengcai, -- 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] Tabulated potentials
Dear all, I want to add the Morse potential ( U=D*[exp(a*(1-r/r0)-2*exp(a/2*(1-r/r0)] ) for nonbonded interactions between CH4-CH4. So, I made three table files to correspond to the interactions between H-H, C-H, and C-C, and I changed vdwtype=user ,Dispcorr=no , energrps = C H , and energrps_table = C C C H H H. However, when I used NVT ensemble to calculate the pressure of pure methane system, I didnot get accurate pressure, actually the pressure is about 20 MPa smaller than the experiment value. Could you give me some suggestions about what is wrong with my set or what I missed in adding the table? Sincerely yours, Zhengcai, -- 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] Tabulated potentials
Dear GROMACS users and developers, I am using GROMACS 5.0.1. I would like to use tabulated potentials (Aziz ones for argon and krypton in particular); as a starting test, I began with LJ tabulated potential. I followed the instructions on the manual, and I did well because my .xvg file of Lennard-Jones 6-12 was substantially identical to the one provided in /share/gromacs/top/table6-12.xvg. I set the .top file and .mdp file according to the instructions on the website and on the manual, besides following the attached pdf in http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated. .top [ defaults ] section has nbfunc and comb-rule equal to 1; C and A parameters in the [ atomtypes ] sections are set equal to 4 epsilon sigma^6 and 4 epsilon sigma^12 respectively. .mdp parameters are: cutoff-scheme = group, coulombtype = user and vdwtype = user. My system is a molecular system of 256 argon atoms. PBC = xyz, no long-range dispersion corrections. Until now, all worked fine. The problems began when I decided to freeze a group of atoms in my system. I added the right atom numbers to the index file, and add energy group exclusions in the .mdp file. Moreover, I specified in the .mdp that I wanted the motion frozen in the 3 directions. The problem is that ordinary LJ of GROMACS (not tabulated) goes on well, and the system solidifies around the frozen seed (an fcc-like seed of 13 atoms); but, with the same conditions, LJ tabulated (also with the table given in the share/top folder) behaves differently. In particular, frozen atoms seem to repulse very strongly the others, in such a way that a hole creates around the frozen nucleus. Also the g(r) are very different, and while in the first case I obtain a more or less ordered solid, in the latter I obtain a strongly disordered solid. What am I missing? Should I apply particular switches or corrections? Why does GROMACS behaves differently if I give it the same potential, but tabulated in the latter case and not tabulated in the first? The only thing that changed between the two cases is the use of a tabulated interaction instead that LJ GROMACS default. Do you know anything about similar problems with freeze groups? Thanks a lot Francesco Mambretti -- 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] tabulated potentials - cutoff
Thanks for pointing me to this, this could actually work. Cheers Sabine Am 05.05.2014 16:05, schrieb Mark Abraham: I've no idea whether PME-User (read its description!) and enerygrp-table interact in a way useful to you, but it might. You were going to test whether your implementation of your model was working correctly anyway, right? ;-) Mark On Mon, May 5, 2014 at 1:25 PM, Sabine Reisser sabine.reis...@kit.eduwrote: But I cannot have specific interactions between two groups and normal PME for the rest, right? Cheers Sabine Am 05.05.2014 10:41, schrieb Mark Abraham: On May 5, 2014 10:01 AM, Sabine Reisser sabine.reis...@kit.edu wrote: So that means the electrostatics are calculated as given in the tables and no long range electrostatics corrections (like PME or RF) are applied? Correct. The .mdp settings determine what interactions are computed; the table just says the values computed. If you wanted PME long-range also, there's a coulombtype for that. Mark Cheers Sabine Am 28.04.2014 18:28, schrieb Justin Lemkul: On 4/28/14, 9:19 AM, Sabine Reisser wrote: Hi, I'm using tabulated potentials to create a hole in a membrane. I define three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the interactions between the dummy atoms and the hydrophobic chains I define an exclusively repulsive potential. All other interactions are defined normally (Coulomb, 6-12 LJ potentials). The 2 dummy atoms are placed on top and below the lipid bilayer, directly over each other. Then I use the pull code to pull the two dummy-atoms towards each other, thereby repelling the hydrophobic lipid chains and opening a pore. This works. But I couldn't figure out how the long range interactions are treated. I assumed only interactions are counted where the distance between atoms is within the range defined in my tables. However, I do define a cutoff radius max(rcoulomb, rvdw), I will call it rcutoff now. In the tables, I have to define values up to rcutoff+1. Is this cutoff radius only to tell GROMACS to expect values up to rcutoff+1? So everything until rcutoff+1 is calculated explicitly after the tables and everything beyond is ignored? I'm asking because usually membranes are quite sensitive to these cutoff values. I would assume that I would see clear changes in e.g. the area per lipid if I simulated long enough. The nonbonded cutoff is whatever you set it to in the .mdp file. The table-extension value is for bookkeeping and neighbor searching purposes. It doesn't change the way the short-range forces are calculated. -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. -- 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] tabulated potentials - cutoff
So that means the electrostatics are calculated as given in the tables and no long range electrostatics corrections (like PME or RF) are applied? Cheers Sabine Am 28.04.2014 18:28, schrieb Justin Lemkul: On 4/28/14, 9:19 AM, Sabine Reisser wrote: Hi, I'm using tabulated potentials to create a hole in a membrane. I define three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the interactions between the dummy atoms and the hydrophobic chains I define an exclusively repulsive potential. All other interactions are defined normally (Coulomb, 6-12 LJ potentials). The 2 dummy atoms are placed on top and below the lipid bilayer, directly over each other. Then I use the pull code to pull the two dummy-atoms towards each other, thereby repelling the hydrophobic lipid chains and opening a pore. This works. But I couldn't figure out how the long range interactions are treated. I assumed only interactions are counted where the distance between atoms is within the range defined in my tables. However, I do define a cutoff radius max(rcoulomb, rvdw), I will call it rcutoff now. In the tables, I have to define values up to rcutoff+1. Is this cutoff radius only to tell GROMACS to expect values up to rcutoff+1? So everything until rcutoff+1 is calculated explicitly after the tables and everything beyond is ignored? I'm asking because usually membranes are quite sensitive to these cutoff values. I would assume that I would see clear changes in e.g. the area per lipid if I simulated long enough. The nonbonded cutoff is whatever you set it to in the .mdp file. The table-extension value is for bookkeeping and neighbor searching purposes. It doesn't change the way the short-range forces are calculated. -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.
Re: [gmx-users] tabulated potentials - cutoff
On May 5, 2014 10:01 AM, Sabine Reisser sabine.reis...@kit.edu wrote: So that means the electrostatics are calculated as given in the tables and no long range electrostatics corrections (like PME or RF) are applied? Correct. The .mdp settings determine what interactions are computed; the table just says the values computed. If you wanted PME long-range also, there's a coulombtype for that. Mark Cheers Sabine Am 28.04.2014 18:28, schrieb Justin Lemkul: On 4/28/14, 9:19 AM, Sabine Reisser wrote: Hi, I'm using tabulated potentials to create a hole in a membrane. I define three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the interactions between the dummy atoms and the hydrophobic chains I define an exclusively repulsive potential. All other interactions are defined normally (Coulomb, 6-12 LJ potentials). The 2 dummy atoms are placed on top and below the lipid bilayer, directly over each other. Then I use the pull code to pull the two dummy-atoms towards each other, thereby repelling the hydrophobic lipid chains and opening a pore. This works. But I couldn't figure out how the long range interactions are treated. I assumed only interactions are counted where the distance between atoms is within the range defined in my tables. However, I do define a cutoff radius max(rcoulomb, rvdw), I will call it rcutoff now. In the tables, I have to define values up to rcutoff+1. Is this cutoff radius only to tell GROMACS to expect values up to rcutoff+1? So everything until rcutoff+1 is calculated explicitly after the tables and everything beyond is ignored? I'm asking because usually membranes are quite sensitive to these cutoff values. I would assume that I would see clear changes in e.g. the area per lipid if I simulated long enough. The nonbonded cutoff is whatever you set it to in the .mdp file. The table-extension value is for bookkeeping and neighbor searching purposes. It doesn't change the way the short-range forces are calculated. -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] tabulated potentials - cutoff
Hi, I'm using tabulated potentials to create a hole in a membrane. I define three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the interactions between the dummy atoms and the hydrophobic chains I define an exclusively repulsive potential. All other interactions are defined normally (Coulomb, 6-12 LJ potentials). The 2 dummy atoms are placed on top and below the lipid bilayer, directly over each other. Then I use the pull code to pull the two dummy-atoms towards each other, thereby repelling the hydrophobic lipid chains and opening a pore. This works. But I couldn't figure out how the long range interactions are treated. I assumed only interactions are counted where the distance between atoms is within the range defined in my tables. However, I do define a cutoff radius max(rcoulomb, rvdw), I will call it rcutoff now. In the tables, I have to define values up to rcutoff+1. Is this cutoff radius only to tell GROMACS to expect values up to rcutoff+1? So everything until rcutoff+1 is calculated explicitly after the tables and everything beyond is ignored? I'm asking because usually membranes are quite sensitive to these cutoff values. I would assume that I would see clear changes in e.g. the area per lipid if I simulated long enough. Cheers Sabine -- 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] tabulated potentials - cutoff
On 4/28/14, 9:19 AM, Sabine Reisser wrote: Hi, I'm using tabulated potentials to create a hole in a membrane. I define three groups: 2 dummy-atoms, all hydrophobic lipid chains, and rest. For the interactions between the dummy atoms and the hydrophobic chains I define an exclusively repulsive potential. All other interactions are defined normally (Coulomb, 6-12 LJ potentials). The 2 dummy atoms are placed on top and below the lipid bilayer, directly over each other. Then I use the pull code to pull the two dummy-atoms towards each other, thereby repelling the hydrophobic lipid chains and opening a pore. This works. But I couldn't figure out how the long range interactions are treated. I assumed only interactions are counted where the distance between atoms is within the range defined in my tables. However, I do define a cutoff radius max(rcoulomb, rvdw), I will call it rcutoff now. In the tables, I have to define values up to rcutoff+1. Is this cutoff radius only to tell GROMACS to expect values up to rcutoff+1? So everything until rcutoff+1 is calculated explicitly after the tables and everything beyond is ignored? I'm asking because usually membranes are quite sensitive to these cutoff values. I would assume that I would see clear changes in e.g. the area per lipid if I simulated long enough. The nonbonded cutoff is whatever you set it to in the .mdp file. The table-extension value is for bookkeeping and neighbor searching purposes. It doesn't change the way the short-range forces are calculated. -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.
[gmx-users] tabulated potentials on GPU?
Dear Gromacs Users, Can you please write me whther Gromacs 4.6 support tabulated potentials for bonded and non-bonded interactions? Steven -- 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] tabulated potentials on GPU?
On Tue, Jan 21, 2014 at 1:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Tabulated, yes. With all algorithms, who knows? Tabulated non-bondeds on GPU, I highly doubt. GPUs are for computing, not looking up random-access tables. Actually, the CUDA Ewald non-bonded kernels are tabulated on Fermi GPUs - the texture memory is pretty good at scattered loads (especially when fully cached)! User-provided tables are not supported, though. Mark On Tue, Jan 21, 2014 at 12:19 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gromacs Users, Can you please write me whther Gromacs 4.6 support tabulated potentials for bonded and non-bonded interactions? Steven -- 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.
