Re: [gmx-users] [EXTERNAL] Re: Lincs warning and Bond length not finite
OPLS tends to be a common choice for graphene. That being said, if you really want to use gromos (for some reason), be sure (as Alex has stated) to make sure that the graphene edges match across the PBC otherwise do not use PBC (but then be sure to change your electrostatics appropriately and make sure the sheet is sufficiently large). -micholas -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Alex Sent: Sunday, May 3, 2020 9:04 PM To: gmx-us...@gromacs.org Subject: [EXTERNAL] Re: [gmx-users] Lincs warning and Bond length not finite You have pressure scaling and LINCS convergence issues, suggesting that the starting configuration is far from equilibrium, as well as potentially other issues. Gromos FF is not appropriate for graphene, and neither is turning C-C bonds into LINCS constraints, as set by your 'all-bonds' -- graphene is not a small organic molecule or a protein. Also, if your system is periodic in all directions, make sure the graphene edges are crystallographically commensurate with respect to PBC and the box size is appropriate. Finally, make sure that the small molecules you're depositing on graphene are properly pre-equilibrated. Alex On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote: > Hello everyone, > > I am simulating the evaporation of non protein molecules on a > graphene sheet. I am using gromos force field and hence the lincs > constrain are set to all-bonds. I have done the energy minimization > and NVT successfully without any warnings. During the NPT > equilibiration I got Lincs warning but the NPT equilibiration was > completed to the end. During the md production run, I received lincs > warning and Bond length not finite and sometimes I received " > nonbonded interaction between particles is larger than the table limit 2.437 > nm". > > I have read that this means that my system is blowing up. Hence, I > have read the Blowing up and diagnosing unstable system on gromacs > website, I can't recognize any of the posted issues in my > files/simulation and hence, I can't decide what exactly is the > problem or what should I change (it seems that my system is well > minimized and the temperature and pressure looks fine). I have added > in the below link, the NPT and md logs and .mdp files and pictures > for the potential energy, Temperature, Pressure and Density. > > https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9 > rF > > I have tried the simulation again with none as lincs constrains and > it worked without any errors. > > I think the problem has something to do with the pressure since the > problem started during the NPT, but I don't know how exactly to find the > problem. > Can anyone guide me please what should I change or how should I start ? > > Thanks, > Mohamed -- 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] [EXTERNAL] Lincs warning and Bond length not finite
How did you set up your graphene sheet originally? Also are you treating the sheet as an infinite sheet (using with periodic molecules)? -Micholas -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Mohamed Abdelaal Sent: Sunday, May 3, 2020 8:40 PM To: gmx-us...@gromacs.org; us...@maillist.sys.kth.se Subject: [EXTERNAL] [gmx-users] Lincs warning and Bond length not finite Hello everyone, I am simulating the evaporation of non protein molecules on a graphene sheet. I am using gromos force field and hence the lincs constrain are set to all-bonds. I have done the energy minimization and NVT successfully without any warnings. During the NPT equilibiration I got Lincs warning but the NPT equilibiration was completed to the end. During the md production run, I received lincs warning and Bond length not finite and sometimes I received " nonbonded interaction between particles is larger than the table limit 2.437 nm". I have read that this means that my system is blowing up. Hence, I have read the Blowing up and diagnosing unstable system on gromacs website, I can't recognize any of the posted issues in my files/simulation and hence, I can't decide what exactly is the problem or what should I change (it seems that my system is well minimized and the temperature and pressure looks fine). I have added in the below link, the NPT and md logs and .mdp files and pictures for the potential energy, Temperature, Pressure and Density. https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF I have tried the simulation again with none as lincs constrains and it worked without any errors. I think the problem has something to do with the pressure since the problem started during the NPT, but I don't know how exactly to find the problem. Can anyone guide me please what should I change or how should I start ? Thanks, Mohamed -- 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] apply pH effect on aminoacids
Protonation state of the amino acids are set during execution of pdb2gmx and you can choose yourself what their protonation state is using -inter or any of the other options if you don't want to go through all. http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 4 May 2020 at 02:59, azadeh kordzadeh wrote: > Hi > I gave a topology of a protein with pdb2gmx command in next step I change > protonation some aminoacids but the topology didn't chage. How could I > create new topology? > I need to obtain topology protonated aminoacid from other servers? > Thanks > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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] Lincs warning and Bond length not finite
You have pressure scaling and LINCS convergence issues, suggesting that the starting configuration is far from equilibrium, as well as potentially other issues. Gromos FF is not appropriate for graphene, and neither is turning C-C bonds into LINCS constraints, as set by your 'all-bonds' -- graphene is not a small organic molecule or a protein. Also, if your system is periodic in all directions, make sure the graphene edges are crystallographically commensurate with respect to PBC and the box size is appropriate. Finally, make sure that the small molecules you're depositing on graphene are properly pre-equilibrated. Alex On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote: Hello everyone, I am simulating the evaporation of non protein molecules on a graphene sheet. I am using gromos force field and hence the lincs constrain are set to all-bonds. I have done the energy minimization and NVT successfully without any warnings. During the NPT equilibiration I got Lincs warning but the NPT equilibiration was completed to the end. During the md production run, I received lincs warning and Bond length not finite and sometimes I received " nonbonded interaction between particles is larger than the table limit 2.437 nm". I have read that this means that my system is blowing up. Hence, I have read the Blowing up and diagnosing unstable system on gromacs website, I can't recognize any of the posted issues in my files/simulation and hence, I can't decide what exactly is the problem or what should I change (it seems that my system is well minimized and the temperature and pressure looks fine). I have added in the below link, the NPT and md logs and .mdp files and pictures for the potential energy, Temperature, Pressure and Density. https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF I have tried the simulation again with none as lincs constrains and it worked without any errors. I think the problem has something to do with the pressure since the problem started during the NPT, but I don't know how exactly to find the problem. Can anyone guide me please what should I change or how should I start ? Thanks, Mohamed -- 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] Lincs warning and Bond length not finite
Hello everyone, I am simulating the evaporation of non protein molecules on a graphene sheet. I am using gromos force field and hence the lincs constrain are set to all-bonds. I have done the energy minimization and NVT successfully without any warnings. During the NPT equilibiration I got Lincs warning but the NPT equilibiration was completed to the end. During the md production run, I received lincs warning and Bond length not finite and sometimes I received " nonbonded interaction between particles is larger than the table limit 2.437 nm". I have read that this means that my system is blowing up. Hence, I have read the Blowing up and diagnosing unstable system on gromacs website, I can't recognize any of the posted issues in my files/simulation and hence, I can't decide what exactly is the problem or what should I change (it seems that my system is well minimized and the temperature and pressure looks fine). I have added in the below link, the NPT and md logs and .mdp files and pictures for the potential energy, Temperature, Pressure and Density. https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF I have tried the simulation again with none as lincs constrains and it worked without any errors. I think the problem has something to do with the pressure since the problem started during the NPT, but I don't know how exactly to find the problem. Can anyone guide me please what should I change or how should I start ? Thanks, Mohamed -- 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] Glycosylation of ASN
Hi, Have you tried reducing the timestep in mdp? On Mon, May 4, 2020, 2:52 AM Naba wrote: > Dear users and developers, > > I have spent extensive amount of time to model glycosylated ASN residues > covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using > Amber99SB-ILDN force field. Though there may be easy way to do this > with CHARMM-GUI, I want it for Amber force field for maintaining > consistency of force field usage with respect to the other sets of > simulations I have performed already. > > I have gone through several post on this and planned to give a try. So, > I've extracted a pair of covalently bound ASN and NAG from the PDB file > where they present. I have generated the NAG topology parameters using > GLYCAM_06j-1 force field in Tleap and ACPYPE. I updated aminoacids.rtp, > ffbonded.itp and all required files as instructed in the manual section 5.6 > and it was successful in equilibrations. After completion of NVT and NPT > successfully for 500 ps each, around 7 ns of the production MD, I am > encountered with warnings and ultimately fatal error like following: > > Step 3869783, time 7739.57 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.03, max 0.13 (between atoms 23 and 24) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > 21 22 67.60.1090 0.1090 0.1090 > ... > ... > ... > > for many steps > > and then > > step 3869795: One or more water molecules can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > Segmentation fault (core dumped) > > I checked it repeatedly by minimizing the structure several times using > other software including a series of vacuum minimization with > GROMACS-2019.5 using steepest descent and conjugate gradient minimizers. > But no success. > > Please try to give a way to resolve it. If possible. > > Regards, > Naba > > > Nabajyoti Goswami > > Research Associate > Bioinformatics Infrastructure Facility > Department of Animal Biotechnology > College of Veterinary Science > Khanapara,Guwahati 781022 > Assam, India > -- > 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] question about how to analyze the free energy landscape generated with gmx sham
Dear Gromacs users; I have generated Gibbs free energy landscapes from the two first principal components PC1 and PC2 obtained from Dihedral Principal Component analysis performed using Gromacs. So, now I have a file *"shamlog-1_2.log" *that contain a list of the bins ordered by energy, for example : Minima sorted after energy Minimum 0 at index 40 energy 0.000 Minimum 1 at index 641 energy 0.146 (...) and I have another file *bindex-1_2.ndx* that shows the frames contained in each bin. Now I do not know how to proceed from here. How do I select the best bins? and then how do I select the best frames from those bins? Should I use all the frames of the selected bins and obtain like an average structure? Kindly, Lazaro -- 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] Glycosylation of ASN
Dear users and developers, I have spent extensive amount of time to model glycosylated ASN residues covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using Amber99SB-ILDN force field. Though there may be easy way to do this with CHARMM-GUI, I want it for Amber force field for maintaining consistency of force field usage with respect to the other sets of simulations I have performed already. I have gone through several post on this and planned to give a try. So, I've extracted a pair of covalently bound ASN and NAG from the PDB file where they present. I have generated the NAG topology parameters using GLYCAM_06j-1 force field in Tleap and ACPYPE. I updated aminoacids.rtp, ffbonded.itp and all required files as instructed in the manual section 5.6 and it was successful in equilibrations. After completion of NVT and NPT successfully for 500 ps each, around 7 ns of the production MD, I am encountered with warnings and ultimately fatal error like following: Step 3869783, time 7739.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.03, max 0.13 (between atoms 23 and 24) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 21 22 67.60.1090 0.1090 0.1090 21 22 67.60.1090 0.1090 0.1090 21 22 67.60.1090 0.1090 0.1090 21 22 67.60.1090 0.1090 0.1090 21 22 67.60.1090 0.1090 0.1090 ... ... ... for many steps and then step 3869795: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) I checked it repeatedly by minimizing the structure several times using other software including a series of vacuum minimization with GROMACS-2019.5 using steepest descent and conjugate gradient minimizers. But no success. Please try to give a way to resolve it. If possible. Regards, Naba Nabajyoti Goswami Research Associate Bioinformatics Infrastructure Facility Department of Animal Biotechnology College of Veterinary Science Khanapara,Guwahati 781022 Assam, India -- 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] apply pH effect on aminoacids
Hi I gave a topology of a protein with pdb2gmx command in next step I change protonation some aminoacids but the topology didn't chage. How could I create new topology? I need to obtain topology protonated aminoacid from other servers? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] conformation tensor
gmx distance -oxyz ? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 1 May 2020 at 16:23, Alex wrote: > Dear all, > > I like to calculate the conformation tensor for a mass of a short polymer. > The conformation tensor is defined as c_ij = 3* ( / > <(Re_bulk)^2>), in which Re_i and Re_j are the Cartesian components of the > Re as the end-to-end vector. Several gmx options are available to calculate > the end-to-end distance but not the end-to-end vector. > I wonder if there is a gmx tool to either directly calculate to > conformation tensor or the end-to-end vector to extract the x and y > directions of that vector later on? > > Thank you > Alex > -- > 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.
