Re: [gmx-users] Installation on iPad
Dear Marko, Thank you for your response. Indeed SSH would be already proper help. I am also interested to see whether I can run GROMACS on itself as well. I came through a shell for iPad, called Blink Shell, which seems to be able to cover some aspects of coding, but I am not sure if it would be able to host gmx too. It is paid btw. My best, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Marko Petrovic Sent: zondag 19 april 2020 19:09 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Installation on iPad You can at least run SSH clients on iOS so you can technically edit text files and run commands from it even if the execution is not on the iPad. With Regards Marko Petrovic Educator Computational Science and Technology School of Electrical Engineering and Computer Science KTH Royal Institute of Technology On 18 Apr 2020, at 14:43, Ali Khodayari mailto:ali.khoday...@student.kuleuven.be> > wrote: Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you'll have it on any other MacOS? Of course, considering the new iPad OS released. 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<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. -- 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] Installation on iPad
Dear gmx users, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you'll have it on any other MacOS? Of course, considering the new iPad OS released. 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.
[gmx-users] Installation on iPad?
Dears, I would like to ask whether it is possible to install GROMACS on iPad as well? Obviously I am not trying to run any simulations on it, but to be able to generate the run files and to transfer them to a cluster. Does it work the same way you’ll have it on any other MacOS? Of course, considering the new iPad OS released. 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
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
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.
[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.
[gmx-users] question regarding coulomb potential output
Dear all, I have a question regarding the output of the Coulombic energy from the edr file. I am looking at the interactions between two molecules, and trying to analyse the contribution of different interaction types between these two. Since hydrogen bonds are formed based on the charge differences between donors and acceptors, I am wondering whether the coulomb potential which I get from the edr file also contains the hydrogen bond energies. Thank you for your kind responses. 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.
[gmx-users] order of atoms in the index file
Hello all, I am trying to calculate the dihedral angels of a group of atoms in a molecule. As I am only interested in part of the molecule, I have manually made an index file containing the desired atoms in groups using gmx make_ndx. Yet, the atom's number in each group is in ascending order. Means that instead of having orders of 858 855 875 865, as expected, I get 855 858 865 875. Is there any way to fix the order of atoms based on selecting procedure while the index file is being made? Obviously it has a great difference on the calculation of dihedral angles. P.S. I am not using gmx mk_angndx as there are dihedral similarities in the system, and I need to exclude them. 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.
[gmx-users] regarding solvating a molecule
Dear all, I am trying to solvate a molecule. I am using GLYCAM force field and have generated the *.gro and *.top files through acpype. I want to include tip3p parameter sets from amber99sb.ff. Including the tip3p.itp in the topology file does not suffice as it complains about OW atomtype not found. What am I doing wrong? How can I include the water molecule in my system? Thank you in advanced. 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.
[gmx-users] Defining a new molecule type
Dear Users, I am trying to use the free energy code to partially shut down the non-bonded interactions in part of my system. I only want to decouple interaction in some part of my system, I have put all the desired residues in groups in the index file. What should I indicate for the couple_moltype line? As the system consists of large number of atoms in the same molecule type. Introducing a new molecule type is not possible because the atoms are connected chain-wise and I want to decouple the interactions in the middle of the chain. Thank you for your responses. 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.
[gmx-users] Free Energy code
Dear all, I am quite new to free energy calculation, so I apologize if the questions seem naive and of course they are a lot. My intention is to turn off vdw and coulombic interactions to perform some tempering cycles on my system. There are though some questions: 1- I only want to decouple interaction in some part of my system, I have put all the desired residues in groups in the index file. What should I indicate for the couple_moltype line? As the system consists of large number of atoms in the same molecule type. Introducing a new molecule type is not possible because the atoms are connected chain-wise and I want to decouple the interactions in the middle of the chain. 2- Is it ok if I don't set the charges to zero from the beginning, and proceed with turning them off step by step like what is done for the vdw in the free energy tutorial? 3- We are only interested in the end state where the interactions are off. Can I decrease the number of spacings? Since we are not going to measure the free energy, and we only intent to bring the system to an state where the interactions are excluded for only part of the system. 4- Since we are going to perform multiple tempering simulations, maintaining the state B (non-bonded interactions off), for each temperature change, shall I keep indicating init_lambda_state = "last one, let's say 20" and still maintain the last value of the λ array? So something like: 0.00 0.05 0.10 . 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00? Thank you for your responses, and sorry for the long email. 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] Bond breakage modelling
Thank you Peter, I will try to have a detailed look. Regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Peter Kroon Sent: dinsdag 19 februari 2019 13:41 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Bond breakage modelling I've never done it myself, so not really. The manual should help :) I don't know if Morse potentials come built-in, or that you'll need to make tables. Be aware that if you have three or more morse potential particles together they can and will form stable triangles, because there is no influence of the angle on the potential. Peter On 19-02-19 13:35, Ali Khodayari wrote: > Dear Peter, > > Thank you for your prompt reply. > I think I can try the morse potential to see how the system responds. > Could you kindly provide some more info about how to implement it? > Best regards, > Ali > > > >> On 19 Feb 2019, at 11:35, Peter Kroon wrote: >> >> Hi Ali, >> >> >> The short answer is "not really". You could model your bonds as >> non-bonded (morse) potentials, but then you lose all angle dependence >> on the potential energy, since the non-bonded potentials must be pair-wise. >> Depending on the exact problem this may be acceptable though. The >> angle dependence on the potential energy also immediately points out >> an issue with your cut-off based approach: how will you deal with the angle(s)? >> >> In literature I have seen some papers of people pulling proteins >> apart, breaking cystein bridges. Those may contain some insight/ideas. >> >> >> Peter >> >>> On 19-02-19 11:28, Ali Khodayari wrote: >>> Dear All, >>> >>> >>> >>> We have simulated a cellulose fiber using GLYCAM06 ff parameters >>> converted to GROMACS. The model is validated and works properly. >>> >>> We are investigating the behavior of the material under tensile load. >>> However, as covalent bonds are modelled with a harmonic potential >>> -as it is in most of the non-reactive force fields- some parameters >>> cannot be extracted. Is there any way to mimic the breakage of the >>> bonds, let's say when the distance of the atoms exceed a certain >>> amount? In other words, if we have a rough idea of the strain at >>> which bonds break, can GROMACS neglect bonds from a certain cut-off onwards? >>> >>> Thank you in advanced for your responses. >>> >>> 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] Bond breakage modelling
Dear Paul, Thank you for your response. Unfortunately, ReaxFF shows some discrepancies in some cases when it comes to carbohydrates. Besides, its parameters are not written for GROMACS. I am looking for maybe a code to mimic this behavior using the validated force fields for carbohydrates, say GROMOS or else. Kind regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Paul Bauer Sent: dinsdag 19 februari 2019 13:43 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Bond breakage modelling Hello, in general I would advise not to use a classical force field to model a quantum mechanical effect like breaking a bond. Classical force fields are not parametrized to reproduce those effects, and while you might get something that looks fine with the morse potential it would definitely be unphysical. If you want to study quantum effects, use a QM method for the parts that are involved in bond breaking, or use a reactive force field like ReaxFF. Cheers Paul On 2019-02-19 13:35, Ali Khodayari wrote: > Dear Peter, > > Thank you for your prompt reply. > I think I can try the morse potential to see how the system responds. > Could you kindly provide some more info about how to implement it? > Best regards, > Ali > > > >> On 19 Feb 2019, at 11:35, Peter Kroon wrote: >> >> Hi Ali, >> >> >> The short answer is "not really". You could model your bonds as >> non-bonded (morse) potentials, but then you lose all angle dependence >> on the potential energy, since the non-bonded potentials must be pair-wise. >> Depending on the exact problem this may be acceptable though. The >> angle dependence on the potential energy also immediately points out >> an issue with your cut-off based approach: how will you deal with the angle(s)? >> >> In literature I have seen some papers of people pulling proteins >> apart, breaking cystein bridges. Those may contain some insight/ideas. >> >> >> Peter >> >>> On 19-02-19 11:28, Ali Khodayari wrote: >>> Dear All, >>> >>> >>> >>> We have simulated a cellulose fiber using GLYCAM06 ff parameters >>> converted to GROMACS. The model is validated and works properly. >>> >>> We are investigating the behavior of the material under tensile load. >>> However, as covalent bonds are modelled with a harmonic potential >>> -as it is in most of the non-reactive force fields- some parameters >>> cannot be extracted. Is there any way to mimic the breakage of the >>> bonds, let's say when the distance of the atoms exceed a certain >>> amount? In other words, if we have a rough idea of the strain at >>> which bonds break, can GROMACS neglect bonds from a certain cut-off onwards? >>> >>> Thank you in advanced for your responses. >>> >>> Kind regards, >>> >>> Ali >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Readhttp://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 togmx-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] Bond breakage modelling
Dear Peter, Thank you for your prompt reply. I think I can try the morse potential to see how the system responds. Could you kindly provide some more info about how to implement it? Best regards, Ali > On 19 Feb 2019, at 11:35, Peter Kroon wrote: > > Hi Ali, > > > The short answer is "not really". You could model your bonds as > non-bonded (morse) potentials, but then you lose all angle dependence on > the potential energy, since the non-bonded potentials must be pair-wise. > Depending on the exact problem this may be acceptable though. The angle > dependence on the potential energy also immediately points out an issue > with your cut-off based approach: how will you deal with the angle(s)? > > In literature I have seen some papers of people pulling proteins apart, > breaking cystein bridges. Those may contain some insight/ideas. > > > Peter > >> On 19-02-19 11:28, Ali Khodayari wrote: >> Dear All, >> >> >> >> We have simulated a cellulose fiber using GLYCAM06 ff parameters converted >> to GROMACS. The model is validated and works properly. >> >> We are investigating the behavior of the material under tensile load. >> However, as covalent bonds are modelled with a harmonic potential -as it is >> in most of the non-reactive force fields- some parameters cannot be >> extracted. Is there any way to mimic the breakage of the bonds, let's say >> when the distance of the atoms exceed a certain amount? In other words, if >> we have a rough idea of the strain at which bonds break, can GROMACS neglect >> bonds from a certain cut-off onwards? >> >> Thank you in advanced for your responses. >> >> 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] Bond breakage modelling
Dear All, We have simulated a cellulose fiber using GLYCAM06 ff parameters converted to GROMACS. The model is validated and works properly. We are investigating the behavior of the material under tensile load. However, as covalent bonds are modelled with a harmonic potential -as it is in most of the non-reactive force fields- some parameters cannot be extracted. Is there any way to mimic the breakage of the bonds, let's say when the distance of the atoms exceed a certain amount? In other words, if we have a rough idea of the strain at which bonds break, can GROMACS neglect bonds from a certain cut-off onwards? Thank you in advanced for your responses. 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] turning off non-bonded terms
Thank you Justin. Kind regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: dinsdag 22 januari 2019 15:59 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] turning off non-bonded terms On 1/22/19 9:37 AM, Ali Khodayari wrote: > Dear Users, > > Does it make sense if I use rcoulomb = 0 and rvdw = 0 in order to turn > off non-bonded term calculation during mdrun? If not, is there any > recommendations? That does the opposite - setting cutoffs to zero calculates *all* nonbonded interactions. If you want to turn them off, you need to use the free energy settings with a lambda state that specifies interactions are off. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] turning off non-bonded terms
Dear Users, Does it make sense if I use rcoulomb = 0 and rvdw = 0 in order to turn off non-bonded term calculation during mdrun? If not, is there any recommendations? Thank you for your responses in advanced. 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] regarding editconf
Thank you Justin. I try to search more for the reason. My best, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: dinsdag 15 januari 2019 16:10 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] regarding editconf On 1/15/19 9:34 AM, Ali Khodayari wrote: > Thank you for your response Justin! > I don't really see how it can cause an error, while it might be just a > visualization defect in VMD. > Previously, I tried to perform each step separately, like doing a > centering by -center 0 0 0, but even performing this step leads to the error "step 0: > Water molecule starting at atom 40225 can not be settled." The only > difference would be a change in the coordinates, no? It is not due to > the fact that I am using 5.1.2 version, is it? Systems can become unstable for any number of reasons, but not simply because some part of a protein appears to be protruding into space. That's just normal PBC. 5.1.2 is very old but I don't know of any specific reason why it should cause a problem. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding editconf
Thank you for your response Justin! I don't really see how it can cause an error, while it might be just a visualization defect in VMD. Previously, I tried to perform each step separately, like doing a centering by -center 0 0 0, but even performing this step leads to the error "step 0: Water molecule starting at atom 40225 can not be settled." The only difference would be a change in the coordinates, no? It is not due to the fact that I am using 5.1.2 version, is it? Best regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: dinsdag 15 januari 2019 15:01 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] regarding editconf On 1/15/19 7:46 AM, Ali Khodayari wrote: > Dear users, > > > > I am trying to reorient and re-center my solute using editconf. > Performing such I can place the structure at the desired place, yet it > is outside the box when I visualize it in VMD. It leads to an error > after mdrun complaining about a water molecule not being settled. > > Here is the command I use: > > $ gmx editconf -f cell.gro -o cell_newbox.gro -princ -bt triclinic -c > -center 0 0 0 -rotate 0 350 0 -n ndx.ndx > > Do you see where the problem is? First, there is no such thing as "outside" an infinite box, so that should not be the cause of any actual problem. Regarding editconf, you're doing too many things at once, which may be mutually exclusive, so you may not be getting what you want. You're telling editconf to align the longest axis along x (with -princ) but also to rotate about y (-rotate 0 350 0). Don't do both of those at once. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding editconf
Dear users, I am trying to reorient and re-center my solute using editconf. Performing such I can place the structure at the desired place, yet it is outside the box when I visualize it in VMD. It leads to an error after mdrun complaining about a water molecule not being settled. Here is the command I use: $ gmx editconf -f cell.gro -o cell_newbox.gro -princ -bt triclinic -c -center 0 0 0 -rotate 0 350 0 -n ndx.ndx Do you see where the problem is? 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.
[gmx-users] Local stress tensors
Dear all, I am trying to extract the local stress tensors for a system undergone a tensile (using the pull code). Can anyone tell me which output (maybe from edr file) can be related to the local stresses? The aim is to achieve the stress-strain curves of crystalline cellulose, in reality. Thank you for your responses. Best, 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] Regarding trjconv
Thank you Justin. I tried to define a reference group having the desired orientation and use -fit. But the box rotates as well. I need to keep the box as it is and just rotate the solute. Using -fit prompts me to choose the group for least squares fit and the output, only. When I use -princ in editconf, it orients the crystal in z direction perfectly. The only problem is that the box rotates as well, and is not well aligned along the same direction. Any suggestions? Best, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: zondag 2 december 2018 17:38 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Regarding trjconv On 12/2/18 11:22 AM, Ali Khodayari wrote: > Dear all, > > > > I am trying to re-center and re-orient an md resulted solute in a box. > Yet, I need the box to hold its position and I only need a group of > atoms to align along z-direction. Trjconv centers the group in the box > but the desired sub-group has a slight inclination which is needed to > be oriented along z axis. Is there any particular trick to do this? > Maybe in combination with editconf? > > trjconv -fit with a suitable index group that defines the orientation you want. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding trjconv
Dear all, I am trying to re-center and re-orient an md resulted solute in a box. Yet, I need the box to hold its position and I only need a group of atoms to align along z-direction. Trjconv centers the group in the box but the desired sub-group has a slight inclination which is needed to be oriented along z axis. Is there any particular trick to do this? Maybe in combination with editconf? Best, 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] non-zero total charge
Solved! I checked the topology. However, a qtot of 0.000 was shown at the end of atoms section, yet, 1152 atoms had an extra plus/minus 0.01 charge which added up to 0.001135 extra net charge. Rounding these numbers to zero removed the note, leading to a zero total charge. Nevertheless, I don't have any idea from where they were generated in the beginning! Kind regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: vrijdag 30 november 2018 20:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] non-zero total charge On 11/29/18 1:13 PM, Ali Khodayari wrote: > Dear gmx community, > > > > I am getting a note before performing the energy minimization step, > from grompp that "System has non-zero charge: -0.001135". The system > is a That net charge looks somewhat large to simply be due to rounding error, so check your topology for errors. -Justin > crystalline cellulose, built in Amber, using GLYCAM06 force field and > the topology and coordinate files have been converted to gromacs > format using acpype. The system has zero charges with/without > solvation. How important is this note? Is this a large value or I can > just neglect it and continue with NVT? > > Thank you for your kind replies. > > Best > > Ali > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] non-zero total charge
Dear Justin, Thank you for your reply. I've checked it several time, and "to me" it looks fine. What exactly should be checked. Anything in particular? Best, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: vrijdag 30 november 2018 20:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] non-zero total charge On 11/29/18 1:13 PM, Ali Khodayari wrote: > Dear gmx community, > > > > I am getting a note before performing the energy minimization step, > from grompp that "System has non-zero charge: -0.001135". The system > is a That net charge looks somewhat large to simply be due to rounding error, so check your topology for errors. -Justin > crystalline cellulose, built in Amber, using GLYCAM06 force field and > the topology and coordinate files have been converted to gromacs > format using acpype. The system has zero charges with/without > solvation. How important is this note? Is this a large value or I can > just neglect it and continue with NVT? > > Thank you for your kind replies. > > Best > > Ali > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] non-zero total charge
Dear gmx community, I am getting a note before performing the energy minimization step, from grompp that "System has non-zero charge: -0.001135". The system is a crystalline cellulose, built in Amber, using GLYCAM06 force field and the topology and coordinate files have been converted to gromacs format using acpype. The system has zero charges with/without solvation. How important is this note? Is this a large value or I can just neglect it and continue with NVT? Thank you for your kind replies. Best 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.
[gmx-users] stress-strain using pull code
Dear all, I am trying to compute the stress-strain curves, using the pull code explained in Justin’s tutorial. I want to put my crystalline cellulose (which is solvated in water) under tension force at room temperature, and compute the nano-mechanical properties of the system, e.g. Yield modulus, etc. How can I relate the potential (energies) of the output edr file to this end? In other words, are the output energies, after tension, absolute values or they are relative values to the time when there have been no tension applied yet? How can I obtain the energy values of only a group of my system out of the edr file? Since I assume the output is, by default, the total averaged energies of the system, while I have no interest in contribution of the part coming from water. Best, 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.
[gmx-users] make_ndx and assigning velocities
Dear Gmx users, I have two questions. I am wondering how I can assign residues from different chains to one single index group? Say, residues 50 to 70 of first chain and residues 120 to 140 of the second chain. Secondly, how can I assign velocities to certain groups? For instance, to restrain the positions of one group (V = 0) and to assign a certain velocity (V ~= 0) to another group? Thank you for your help. 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] pdb2gmx fatal error
Dear Justin, Thank you for your full explanation. That made it all clear now. Kind regards, Ali > On 13 Nov 2018, at 00:57, Justin Lemkul wrote: > > > > On 11/8/18 1:37 PM, Ali Khodayari wrote: >> Dear Justin, >> >> Thank you for your response. Yet, I have not been able to solve the problem. >> >> The structure looks fine but gromacs is complaining about a dangling atom at >> one of the terminal ends, if I choose no terminal to be added. While, > > You can't "see" a dangling bond by visualizing the structure. That term > refers exclusively to an incomplete terminus in terms of the *topology* that > is being generated for the system. Maybe atoms are missing or an > inappropriate terminal patch is being applied; either would generate that > error. But again I emphasize the fact that a chain of glucose has first and > last residues that are structurally and topologically different from > internal, linked monomers. It's basic chemistry. > > > >> ATOM 27 O3 GLC02 3.909 5.661 5.002 1.00 0.04 >> O >> ATOM 28 HO4 GLC02 4.850 3.729 10.263 1.00 0.00 >> H >> ATOM 29 O1 GLC01 3.396 2.685 4.467 1.00 0.04 >> O > > Here's your problem - your residue numbers alternate back and forth between 1 > and 2. pdb2gmx ignores these and uses its own numbering, incrementing the > internal counter whenever the residue number changes. So to pdb2gmx, your > input file is full of incomplete residues. > >> ATOM 30 O5 GLC02 4.225 2.770 8.173 1.00 0.04 >> O >> ATOM 31 O6 GLC02 3.558 0.309 5.328 1.00 0.04 >> O >> ATOM 32 H1 GLC02 2.572 4.115 8.609 1.00 0.00 >> H >> ATOM 33 H2 GLC02 5.244 5.151 7.307 1.00 0.00 >> H >> ATOM 34 H3 GLC02 2.361 4.651 6.153 1.00 0.00 >> H >> ATOM 35 H4 GLC02 5.141 3.258 5.636 1.00 0.00 >> H >> ATOM 36 H5 GLC02 2.480 2.262 6.979 1.00 0.00 >> H >> ATOM 37 H61 GLC02 3.879 0.196 7.468 1.00 0.00 >> H >> ATOM 38 H62 GLC02 5.286 0.920 6.494 1.00 0.00 >> H >> ATOM 39 HO2 GLC02 2.496 6.480 7.836 1.00 0.00 >> H >> ATOM 40 HO3 GLC02 5.015 5.674 4.919 1.00 0.00 >> H >> ATOM 41 HO6 GLC02 2.453 0.270 5.418 1.00 0.00 >> H >> ATOM 42 O3 GLC01 3.852 1.653 -0.348 1.00 0.00 >> O > > As above, now you're again going back and forth between 1 and 2, so pdb2gmx > sees a new residue, which is not correct. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx fatal error
Dear Justin, Thank you for your response. Yet, I have not been able to solve the problem. The structure looks fine but gromacs is complaining about a dangling atom at one of the terminal ends, if I choose no terminal to be added. While, assigning a terminal to the ends (which I don't understand why), results to another error, which to me seems bizarre. It is still complaining about an atom (C6) which is not found in the input file (.rtp?), however, it is indeed one of the atoms in the rtp file. Here is what it looks like in the rtp file: [ GLC0 ] [ atoms ] C4 CH1R0.23200 1 O4 OA -0.64200 1 HO4 H 0.41000 1 C3 CH1R0.23200 2 O3OA-0.64200 2 HO3 H 0.41000 2 C2 CH1R0.23200 3 O2OA-0.64200 3 HO2 H 0.41000 3 C6 CH2 0.23200 4 O6OA-0.64200 4 HO6 H 0.41000 4 C5 CH1R0.23200 0 O5OR-0.46400 0 C1 CH1R0.46400 0 O1OE-0.46400 0 And the pdb input file is: ATOM 1 C1 GLC01 3.992 3.199 3.177 1.00 0.04 C ATOM 2 C2 GLC01 3.597 2.204 2.072 1.00 0.04 C ATOM 3 C3 GLC01 4.231 2.633 0.737 1.00 0.04 C ATOM 4 C4 GLC01 3.713 4.036 0.378 1.00 0.04 C ATOM 5 C5 GLC01 4.096 5.017 1.502 1.00 0.04 C ATOM 6 C6 GLC01 3.581 6.419 1.132 1.00 0.04 C ATOM 7 O2 GLC01 4.094 0.828 2.442 1.00 0.04 O ATOM 8 O5 GLC01 3.476 4.569 2.805 1.00 0.04 O ATOM 9 O6 GLC01 4.207 6.834 -0.178 1.00 0.04 O ATOM 10 H1 GLC01 5.128 3.219 3.268 1.00 0.00 H ATOM 11 H2 GLC01 2.462 2.181 1.967 1.00 0.00 H ATOM 12 H3 GLC01 5.366 2.661 0.847 1.00 0.00 H ATOM 13 H4 GLC01 2.578 4.005 0.271 1.00 0.00 H ATOM 14 H5 GLC01 5.230 5.045 1.611 1.00 0.00 H ATOM 15 H61 GLC01 3.858 7.165 1.950 1.00 0.00 H ATOM 16 H62 GLC01 2.449 6.385 1.015 1.00 0.00 H ATOM 17 HO2 GLC01 5.198 0.853 2.551 1.00 0.00 H ATOM 18 HO6 GLC01 5.313 6.850 -0.083 1.00 0.00 H ATOM 19 O4 GLC02 4.312 4.595 9.824 1.00 0.04 O ATOM 20 C1 GLC02 3.708 4.145 8.515 1.00 0.04 C ATOM 21 C2 GLC02 4.109 5.126 7.399 1.00 0.04 C ATOM 22 C3 GLC02 3.497 4.668 6.062 1.00 0.04 C ATOM 23 C4 GLC02 4.005 3.250 5.730 1.00 0.04 C ATOM 24 C5 GLC02 3.616 2.295 6.877 1.00 0.04 C ATOM 25 C6 GLC02 4.151 0.877 6.596 1.00 0.04 C ATOM 26 O2 GLC02 3.601 6.506 7.743 1.00 0.04 O ATOM 27 O3 GLC02 3.909 5.661 5.002 1.00 0.04 O ATOM 28 HO4 GLC02 4.850 3.729 10.263 1.00 0.00 H ATOM 29 O1 GLC01 3.396 2.685 4.467 1.00 0.04 O ATOM 30 O5 GLC02 4.225 2.770 8.173 1.00 0.04 O ATOM 31 O6 GLC02 3.558 0.309 5.328 1.00 0.04 O ATOM 32 H1 GLC02 2.572 4.115 8.609 1.00 0.00 H ATOM 33 H2 GLC02 5.244 5.151 7.307 1.00 0.00 H ATOM 34 H3 GLC02 2.361 4.651 6.153 1.00 0.00 H ATOM 35 H4 GLC02 5.141 3.258 5.636 1.00 0.00 H ATOM 36 H5 GLC02 2.480 2.262 6.979 1.00 0.00 H ATOM 37 H61 GLC02 3.879 0.196 7.468 1.00 0.00 H ATOM 38 H62 GLC02 5.286 0.920 6.494 1.00 0.00 H ATOM 39 HO2 GLC02 2.496 6.480 7.836 1.00 0.00 H ATOM 40 HO3 GLC02 5.015 5.674 4.919 1.00 0.00 H ATOM 41 HO6 GLC02 2.453 0.270 5.418 1.00 0.00 H ATOM 42 O3 GLC01 3.852 1.653 -0.348 1.00 0.00 O ATOM 43 HO3 GLC01 4.305 1.969 -1.311 1.00 0.00 H END The error is given as a result of the command: gmx pdb2gmx -f cellobiose.pdb -o cellobiose.gro -ignh -ter The error: Fatal error: Residue 4 named GLC0 of a molecule in the input file was mapped to an entry in the topology database, but the atom C6 used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Do you have any idea why it is happening? Thank you in advanced. Regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: donderdag 8 november 2018 13:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx fatal error On 11/7/18 1:05 PM, Ali Khodayari wrote: > Dear gmx users, > > > > I am trying to simulate a cellobiose, using GROMOS53a6CARBO. Th
[gmx-users] pdb2gmx fatal error
Dear gmx users, I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom names were modified according to the rtp file of the force field. Yet, I get the following error while I perform pdb2gmx command: Fatal error: Residue 4 named GLC of a molecule in the input file was mapped to an entry in the topology database, but the atom C6 used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed." I also tried to delete the hydrogens in the pdb file but the error changed to the following: Fatal error: Residue 876814369 named GLC of a molecule in the input file was mapped to an entry in the topology database, but the atom C3 used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Ignoring the hydrogens through -ignh will give the first error as well. Then I added the GLC residue to the residuetypes.dat and the error changed to: Fatal error: atom N not found in buiding block 1GLC while combining tdb and rtp Is there anything wrong with the pdb file? Here is the entry of it: ATOM 1 C1 GLC 23.992 3.1993.177 1.00 0.04 C ATOM 2 C2 GLC 23.597 2.2042.072 1.00 0.04 C ATOM 3 C3 GLC 24.231 2.6330.737 1.00 0.04 C ATOM 4 C4 GLC 23.713 4.0360.378 1.00 0.04 C ATOM 5 C5 GLC 24.096 5.0171.502 1.00 0.04 C ATOM 6 C6 GLC 23.581 6.4191.132 1.00 0.04 C ATOM 7 O2 GLC 24.094 0.8282.442 1.00 0.04 O ATOM 8 O5 GLC 23.476 4.5692.805 1.00 0.04 O ATOM 9 O6 GLC 24.207 6.834 -0.178 1.00 0.04 O ATOM 10 H1 GLC 25.128 3.2193.268 1.00 0.00 H ATOM 11 H2 GLC 22.462 2.1811.967 1.00 0.00 H ATOM 12 H3 GLC 25.366 2.6610.847 1.00 0.00 H ATOM 13 H4 GLC 22.578 4.0050.271 1.00 0.00 H ATOM 14 H5 GLC 25.230 5.0451.611 1.00 0.00 H ATOM 15 H61 GLC 23.858 7.1651.950 1.00 0.00 H ATOM 16 H62 GLC 22.449 6.3851.015 1.00 0.00 H ATOM 17 HO2 GLC 25.198 0.8532.551 1.00 0.00 H ATOM 18 HO6 GLC 25.313 6.850 -0.083 1.00 0.00 H ATOM 19 O1 GLC 34.312 4.5959.824 1.00 0.04 O ATOM 20 C1 GLC 33.708 4.1458.515 1.00 0.04 C ATOM 21 C2 GLC 34.109 5.1267.399 1.00 0.04 C ATOM 22 C3 GLC 33.497 4.6686.062 1.00 0.04 C ATOM 23 C4 GLC 34.005 3.2505.730 1.00 0.04 C ATOM 24 C5 GLC 33.616 2.2956.877 1.00 0.04 C ATOM 25 C6 GLC 34.151 0.8776.596 1.00 0.04 C ATOM 26 O2 GLC 33.601 6.5067.743 1.00 0.04 O ATOM 27 O3 GLC 33.909 5.6615.002 1.00 0.04 O ATOM 28 O1 GLC 23.396 2.6854.467 1.00 0.04 O ATOM 29 O5 GLC 34.225 2.7708.173 1.00 0.04 O ATOM 30 O6 GLC 33.558 0.3095.328 1.00 0.04 O ATOM 31 H1 GLC 32.572 4.1158.609 1.00 0.00 H ATOM 32 H2 GLC 35.244 5.1517.307 1.00 0.00 H ATOM 33 H3 GLC 32.361 4.6516.153 1.00 0.00 H ATOM 34 H4 GLC 35.141 3.2585.636 1.00 0.00 H ATOM 35 H5 GLC 32.480 2.2626.979 1.00 0.00 H ATOM 36 H61 GLC 33.879 0.1967.468 1.00 0.00 H ATOM 37 H62 GLC 35.286 0.9206.494 1.00 0.00 H ATOM 38 HO2 GLC 32.496 6.4807.836 1.00 0.00 H ATOM 39 HO3 GLC 35.015 5.6744.919 1.00 0.00 H ATOM 40 HO6 GLC 32.453 0.2705.418 1.00 0.00 H ATOM 41 O3 GLC 23.852 1.653 -0.348 1.00 0.00 O ATOM 42 HO3 GLC 24.305 1.969 -1.311 1.00 0.00 H TER 43 END P.S.: The file is well written and doesn't look like the one above, as far as the column arrangement is concerned. 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] ACPYPE not working.
Have you tried to source amber before commanding acpype for the conversion? Apparently it’s looking for antechamber but it can’t access it. When amber is sourced first, you can get a result from commands such as antechamber -h Try to first source your amber, and then run acpype. > On 1 Nov 2018, at 09:52, neelam wafa wrote: > > Hi! > Dear all > I am using acpype to generate topologies of ligand for gromacs md > simmulation. I habe amber tools 18 and downloaded acpype from github. The > test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c > gas or even > ../acpype.py -di UNL.mol2 > iI get following error > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > Weird atomic valence (2) for atom (ID: 1, Name: C). > Possible open valence. > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > File "../acpype.py", line 3704, in > File "../acpype.py", line 3392, in __init__ > File "../acpype.py", line 910, in setResNameCheckCoords > Total time of execution: less than a second > Please any way to get out of this problem? Looking forward for your > cooperation > Regards > -- > 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] GLYCAM for gromacs
Dear gmx users, We are trying to simulate polysaccharides, cellulose and hemicellulose in particular, in GROMACS. The intention is to use GLYCAM forcefield parameters as well. My question is, is there any properly quick way to parametrize GLYCAM force field to be used in GROMACS? Moreover, is it feasible to manually write the raw force field parameters (GLYCAM_06j.dat) in GROMACS language? Let's say, using a python script? Or it leads to any further problems? 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.
