Re: [gmx-users] GROMACS mailing-list will move to a forum
Hello gmx users! As announced in my previous message at the beginning of the week, we will be activating the new discussion forum today. At the same time, the mailing list will move to read-only mode, so please don't be surprised when it is no longer possible to submit new messages to it. :) As a reminder, you can sign up to the forum here: https://gromacs.bioexcel.eu/ Again, we are looking forward to interact with the community in this new way, and hope it will make it easier for you to solve issues that you have while using GROMACS. Cheers Paul On 04/05/2020 15:51, Paul bauer wrote: Hello again @ all gmx-users! A month has passed and we have moved forward with our work to move the user mailing list to the [discussion forum] https://gromacs.bioexcel.eu/. The discussion forum will open Friday, 8 May 2020. We are now ready to accept people signing up to the forum at https://gromacs.bioexcel.eu/. We will start allowing new posts starting from Friday to give people some time to get used to the forum settings. At the same time (Friday), the gmx-users mailinglist will be set in read-only mode. We are looking forward to engaging with you in this new format and hope it will help the community to solve user issues with GROMACS. Cheers Paul On 01/04/2020 14:06, Paul bauer wrote: Hello gmx-users! We have been working behind the scenes the last few months on some changes to the organization of the GROMACS project, one of them is switching our gmx-users mailing list to a forum We are continuously re-thinking about how we can best engage with you and how people can get the best help when it comes to questions about using GROMACS for different scientific problems. While the user list has worked well for this in the past, it has also shown some deficiencies, mostly in finding already existing questions and the correct answers for them. To hopefully change this in the future we are now in the process of moving the existing list to use a Discourse forum instead that will be made public in the beginning of May. At the switching point, the current list will be read only (and the archive will be kept alive) so people will still be able to search it in the future for existing answers, but won't be able to post any new questions. The forum will still support the pure email based conversation if you prefer this kind of interaction, but it will also allow ranking of responses and make it easier to see which answers are coming from whom. You will have the opportunity to sign up for the forum when it goes live and I'll send a reminder for it when the time comes. Cheers Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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 parameters for simulation annealing
Dear Gromacs users, I am trying to run a simulation annealing using Gromacs of a small molecule. Does anybody knows if there is a protocol to set up the annealing parameters for Gromacs; initial temperature, final temperature, annealing-npoints, annealing-ntimes and the annealing-temp? My total simulation time is 10ns and I collect frames every 200 fs. 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.
Re: [gmx-users] gmx distance com error
Cs : : : : : / **:***/ / **:/ /**/ I tried to visualize my problem that I asked. Cs is the atom which I have fixed at a certain distance from the clay sheet as shown below (containing 192 surface oxygen). I am performing umbrella sampling and using pull code to pull the particular Cs atom at a given rate in z direction. I just want to calculate distance of my Cs atom from the center of mass (com) of the clay sheet as shown above. Thank you, Regards, Debashish On Thu, May 7, 2020 at 8:51 PM Debashish Banerjee wrote: > Hello gmx users, > > I am stuck at a very basic command line and need your expertise in dealing > through it. > > Basically, I have a clay sheet containing 192 surface oxygen. Since I am > doing umbrella sampling for PMF calculations, I want to get the progression > of COM distances of my fixed Cs atom from the center of mass of the clay > sheet (basically these 192 surface oxygen) over time. > > I have already created special index file which has relevant groups such > as ; > group 18 --> *referenceSurface* ~containing 192 surface oxygen > group 19 --> *restrainedCs* ~containing 1 Cs atom (basically the one that > I have fixed) > group 20 --> another Cs atom (this one is not fixed and can move freely in > all sample space during the entire course of simulation) > > Command line: > > *Case 1* > > *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of > group 19 plus com of group 18' -oxyz dist00.xvg* > > Inconsistency in user input: > Invalid index group reference(s) > Group 'referenceSurface' cannot be used in selections except as a full > value > of the selection, because atom indices in it are not sorted and/or it > contains duplicate atoms. > > *Case 2* > *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of > group 19 plus com of group 20' -oxyz dist2.xvg* > > Reading file npt.tpr, VERSION 2016.4 (single precision) > Reading frames from gro file 'Generated by trjconv : clay + Cs + acetate + > water t= 2.0', 24221 atoms. > Last frame 0 time2.000 > Analyzed 1 frames, last time 2.000 > com of group 19 plus com of group 20: > Number of samples: 1 > Average distance: 0.52370 nm > Standard deviation: 0.0 nm > > My understanding is that if I compare the above 2 cases, I would say that > for *case 2*, Cs is measuring it's distance from the only other Cs atom. > No problem here, whereas for *case 1*, Cs atom is measuring it's distance > from all 192 oxygen atoms, somehow not understanding how to take the center > of mass of the whole sheet containing 192 atoms. > > Approach taken: > 1. Modified my command line from this: > gmx_mpi distance -s pull.tpr -f conf0.gro -n index.ndx -select 'com of > group "restrainedCs" plus com of group "referenceSurface"' -oall dist0.xvg > 2. Used all output options like -oav / -oxyz > > I have followed the following threads, but still couldn't manage to > rectify this error > > https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg16576.html > > > https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg30552.html > > > Please help. I am pretty much sure that I am overseeing a very basic step. > > -- > *Best Regards* > > *Debashish Banerjee* > > *Ph.D. (Nuclear Materials, Subatech)* > *MS(Sustainable Nuclear Engineering)* > *Advance Nuclear Waste Management* > *Institut Mines-Telecom, **France* > -- *Best Regards* *Debashish Banerjee* *Ph.D. (Nuclear Materials, Subatech)* *MS(Sustainable Nuclear Engineering)* *Advance Nuclear Waste Management* *Institut Mines-Telecom, **France* -- 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] Negative part of the reaction coordinate in PMF
Dear all, In a PMF simulation using WHAM, the windows are somehow that the reaction coordinate (RC = COM_group1 COM_group2) should have both positive and negative parts along Z direction, e.g COM_group1 locates in the middle of the reaction coordinate more or less. However, what the WHAM gives out is only the positive part of the RC, while all the .tpr and pullf.xvg files for the whole RC are available. I wonder how I can have PMF along the whole reaction coordinate in this case? Of course, one possible solution might be to run WHAM separately on windows of positive and negative parts of reaction coordinate and then merge the two profiles in a single profile later. But what I found out unexpectedly is that presence of each part (e.g negative part) in gmx WHAM, would affect on the PMF of the another part so that the PMF of the only positive part varies when the windows of the negative part are and are not considered. The -sym yes flag doesn't help as the two end points of the RC don't overlap each other. 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.
[gmx-users] gmx distance com error
Hello gmx users, I am stuck at a very basic command line and need your expertise in dealing through it. Basically, I have a clay sheet containing 192 surface oxygen. Since I am doing umbrella sampling for PMF calculations, I want to get the progression of COM distances of my fixed Cs atom from the center of mass of the clay sheet (basically these 192 surface oxygen) over time. I have already created special index file which has relevant groups such as ; group 18 --> *referenceSurface* ~containing 192 surface oxygen group 19 --> *restrainedCs* ~containing 1 Cs atom (basically the one that I have fixed) group 20 --> another Cs atom (this one is not fixed and can move freely in all sample space during the entire course of simulation) Command line: *Case 1* *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of group 19 plus com of group 18' -oxyz dist00.xvg* Inconsistency in user input: Invalid index group reference(s) Group 'referenceSurface' cannot be used in selections except as a full value of the selection, because atom indices in it are not sorted and/or it contains duplicate atoms. *Case 2* *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of group 19 plus com of group 20' -oxyz dist2.xvg* Reading file npt.tpr, VERSION 2016.4 (single precision) Reading frames from gro file 'Generated by trjconv : clay + Cs + acetate + water t= 2.0', 24221 atoms. Last frame 0 time2.000 Analyzed 1 frames, last time 2.000 com of group 19 plus com of group 20: Number of samples: 1 Average distance: 0.52370 nm Standard deviation: 0.0 nm My understanding is that if I compare the above 2 cases, I would say that for *case 2*, Cs is measuring it's distance from the only other Cs atom. No problem here, whereas for *case 1*, Cs atom is measuring it's distance from all 192 oxygen atoms, somehow not understanding how to take the center of mass of the whole sheet containing 192 atoms. Approach taken: 1. Modified my command line from this: gmx_mpi distance -s pull.tpr -f conf0.gro -n index.ndx -select 'com of group "restrainedCs" plus com of group "referenceSurface"' -oall dist0.xvg 2. Used all output options like -oav / -oxyz I have followed the following threads, but still couldn't manage to rectify this error https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg16576.html https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg30552.html Please help. I am pretty much sure that I am overseeing a very basic step. -- *Best Regards* *Debashish Banerjee* *Ph.D. (Nuclear Materials, Subatech)* *MS(Sustainable Nuclear Engineering)* *Advance Nuclear Waste Management* *Institut Mines-Telecom, **France* -- 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] How to apply position restrain on selected atoms in .gro files in Gromacs?
Hello gmx users, I am stuck at a very basic command line and need your expertise in dealing through it. Basically, I have a clay sheet containing 192 surface oxygen. Since I am doing umbrella sampling for PMF calculations, I want to get the progression of COM distances of my fixed Cs atom from the center of mass of the clay sheet (basically these 192 surface oxygen) over time. I have already created special index file which has relevant groups such as ; group 18 --> *referenceSurface* ~containing 192 surface oxygen group 19 --> *restrainedCs* ~containing 1 Cs atom (basically the one that I have fixed) group 20 --> another Cs atom (this one is not fixed and can move freely in all sample space during the entire course of simulation) Command line: *Case 1* *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of group 19 plus com of group 18' -oxyz dist00.xvg* Inconsistency in user input: Invalid index group reference(s) Group 'referenceSurface' cannot be used in selections except as a full value of the selection, because atom indices in it are not sorted and/or it contains duplicate atoms. *Case 2* *gmx_mpi distance -n index.ndx -f conf0.gro -s pull.tpr -select 'com of group 19 plus com of group 20' -oxyz dist2.xvg* Reading file npt.tpr, VERSION 2016.4 (single precision) Reading frames from gro file 'Generated by trjconv : clay + Cs + acetate + water t= 2.0', 24221 atoms. Last frame 0 time2.000 Analyzed 1 frames, last time 2.000 com of group 19 plus com of group 20: Number of samples: 1 Average distance: 0.52370 nm Standard deviation: 0.0 nm My understanding is that if I compare the above 2 cases, I would say that for *case 2*, Cs is measuring it's distance from the only other Cs atom. No problem here, whereas for *case 1*, Cs atom is measuring it's distance from all 192 oxygen atoms, somehow not understanding how to take the center of mass of the whole sheet containing 192 atoms. Approach taken: 1. Modified my command line from this: gmx_mpi distance -s pull.tpr -f conf0.gro -n index.ndx -select 'com of group "restrainedCs" plus com of group "referenceSurface"' -oall dist0.xvg 2. Used all output options like -oav / -oxyz I have followed the following threads, but still couldn't manage to rectify this error https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg16576.html https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg30552.html Please help. I am pretty much sure that I am overseeing a very basic step. Regards, Debashish On Wed, May 6, 2020 at 12:40 AM Debashish Banerjee wrote: > Thank you Justin, you are a life saver..! > It's working now. You have correctly pointed out the issue. > Thank you so much.. :) > > Regards, > Debashish > > On Wed, May 6, 2020 at 12:11 AM Justin Lemkul wrote: > >> >> >> On 5/5/20 5:54 PM, Debashish Banerjee wrote: >> > Dear gmx users, >> > >> > I have been stuck in a problem for a month now and have scrutinized all >> the >> > past discussions and forms related to it dating as back as 9 years. Now >> I >> > really need your help. >> > >> > My system has Clays (layered philosillacates), Cesium ions (Cs), acetate >> > molecules as well as water. In total 24241 atoms in the whole system. I >> > want to perform free energy calculations *(PMF)* via *umbrella >> sampling*. >> > >> > The whole idea is that I want to fix one Cs atom (atom number/index >> number~ >> > 5790) near to the basal surface (top layer) of clay and put in use of >> the* >> > pull* code as described in umbrella sampling and thereafter perform >> *WHAM* >> > calculations to see the progression of COM distance between (Cs) and >> the >> > surface oxygen's present on the top layer of clay sheet over time. >> > >> > When, I see it in my .gro files, I can find all 16 Cs atoms ranging from >> > index number (5785-5780). I just want to fix a particular single Cs atom >> > (index number 5790) as mentioned above. For this I create a special >> index >> > file which now has an extra group containing just 1 Cs atom. After >> this, I >> > take in the use of gmx genrestr command : >> > *gmx genrestr -f npt.gro -n index.ndx -o posre_Cs.itp -fc 0 0 1000* >> > This commands redirects to the newly created group from the index file >> > which I created above and put constraints in it. >> > >> > *Step 1 * >> > The *posre_Cs.itp* file looks like this: >> > [ position_restraints ] >> > ; ifunct fcxfcyfcz >> > 5790 1 00 1000 >> > >> > * Step 2 * >> > *My topology should include an if statement, so I also define it like >> this:* >> > >> > #include "../charmm36.ff/forcefield.itp" >> > >> > ; include params for ClayFF >> > #include "../ClayFF.ff/ffnonbonded.itp" >> > >> > ; Include topology for Clay Montmorillonite (MMT) >> > #include "../ClayFF.ff/MMT_UC/UC2.itp" >> > #include "../ClayFF.ff/MMT_UC/UC1.itp" >> > #include
Re: [gmx-users] Question on energygrps setting
On 5/7/20 10:57 AM, Devargya Chakraborty wrote: I think I couldn't frame the question correctly. Let's say I have a silica surface and I have water droplet on it and after a proper nvt simulation I want to calculate the interaction energy of the water droplet with the surface then how can I use the energy grps option for analysis. You would specify groups (with an index file or from default groups) e.g. energygrps = SOL Surface -Justin Thanks Devargya Chakraborty On Thu 7 May, 2020, 8:23 PM Justin Lemkul, wrote: On 5/7/20 10:49 AM, Devargya Chakraborty wrote: Suppose my system contains an anion a cation and water and I have done an nvt simulation.after the completion I want to see the energy profile of the individual groups like the cation or the anion etc. Can anybody guide me how to use the energy grps option in analysing that. You wouldn't. The energygrps setting is specifically for computing interaction energies between two groups. It cannot be used to give you the energy of a group. You could do that by extracting coordinates of interest from the trajectory with trjconv, making a matching .tpr with convert-tpr, and then using mdrun -rerun to recompute the energies. While you *can* do this, note that these values will generally have no physical meaning. -Justin Thanks Devargya Chakraborty On Thu 7 May, 2020, 5:48 PM Justin Lemkul, wrote: On 5/6/20 6:31 PM, Lei Qian wrote: Dear users, I know interaction energy calculation is carried out via energygrps setting in mdp file. Because free energy-related settings do not include this energygrps setting, so I think this energygrps setting may NOT be related to free energy settings. Could I ask whether my idea is correct or not? The two have nothing to do with one another. In general, energygrps shouldn't be used during an MD simulation anyway, and should be treated as an analysis method. -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. -- == 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. -- == 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.
Re: [gmx-users] Question on energygrps setting
I think I couldn't frame the question correctly. Let's say I have a silica surface and I have water droplet on it and after a proper nvt simulation I want to calculate the interaction energy of the water droplet with the surface then how can I use the energy grps option for analysis. Thanks Devargya Chakraborty On Thu 7 May, 2020, 8:23 PM Justin Lemkul, wrote: > > > On 5/7/20 10:49 AM, Devargya Chakraborty wrote: > > Suppose my system contains an anion a cation and water and I have done an > > nvt simulation.after the completion I want to see the energy profile of > the > > individual groups like the cation or the anion etc. Can anybody guide me > > how to use the energy grps option in analysing that. > > You wouldn't. The energygrps setting is specifically for computing > interaction energies between two groups. It cannot be used to give you > the energy of a group. > > You could do that by extracting coordinates of interest from the > trajectory with trjconv, making a matching .tpr with convert-tpr, and > then using mdrun -rerun to recompute the energies. While you *can* do > this, note that these values will generally have no physical meaning. > > -Justin > > > Thanks > > Devargya Chakraborty > > > > On Thu 7 May, 2020, 5:48 PM Justin Lemkul, wrote: > > > >> > >> On 5/6/20 6:31 PM, Lei Qian wrote: > >>> Dear users, > >>> > >>> I know interaction energy calculation is carried out via energygrps > >> setting > >>> in mdp file. > >>> Because free energy-related settings do not include this energygrps > >>> setting, so I think this energygrps setting may NOT be related to free > >>> energy settings. > >>> Could I ask whether my idea is correct or not? > >> The two have nothing to do with one another. In general, energygrps > >> shouldn't be used during an MD simulation anyway, and should be treated > >> as an analysis method. > >> > >> -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. > >> > > -- > == > > 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] Question on energygrps setting
On 5/7/20 10:49 AM, Devargya Chakraborty wrote: Suppose my system contains an anion a cation and water and I have done an nvt simulation.after the completion I want to see the energy profile of the individual groups like the cation or the anion etc. Can anybody guide me how to use the energy grps option in analysing that. You wouldn't. The energygrps setting is specifically for computing interaction energies between two groups. It cannot be used to give you the energy of a group. You could do that by extracting coordinates of interest from the trajectory with trjconv, making a matching .tpr with convert-tpr, and then using mdrun -rerun to recompute the energies. While you *can* do this, note that these values will generally have no physical meaning. -Justin Thanks Devargya Chakraborty On Thu 7 May, 2020, 5:48 PM Justin Lemkul, wrote: On 5/6/20 6:31 PM, Lei Qian wrote: Dear users, I know interaction energy calculation is carried out via energygrps setting in mdp file. Because free energy-related settings do not include this energygrps setting, so I think this energygrps setting may NOT be related to free energy settings. Could I ask whether my idea is correct or not? The two have nothing to do with one another. In general, energygrps shouldn't be used during an MD simulation anyway, and should be treated as an analysis method. -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. -- == 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.
Re: [gmx-users] Question on energygrps setting
Suppose my system contains an anion a cation and water and I have done an nvt simulation.after the completion I want to see the energy profile of the individual groups like the cation or the anion etc. Can anybody guide me how to use the energy grps option in analysing that. Thanks Devargya Chakraborty On Thu 7 May, 2020, 5:48 PM Justin Lemkul, wrote: > > > On 5/6/20 6:31 PM, Lei Qian wrote: > > Dear users, > > > > I know interaction energy calculation is carried out via energygrps > setting > > in mdp file. > > Because free energy-related settings do not include this energygrps > > setting, so I think this energygrps setting may NOT be related to free > > energy settings. > > Could I ask whether my idea is correct or not? > > The two have nothing to do with one another. In general, energygrps > shouldn't be used during an MD simulation anyway, and should be treated > as an analysis method. > > -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] Info regarding restrained minimization, equilibration & production
Thanks Justin. I will then add manually the constraints on the topology file. Paolo Il giorno gio 7 mag 2020 alle ore 14:56 Justin Lemkul ha scritto: > > > On 5/7/20 8:53 AM, Paolo Costa wrote: > > Dear Justin > > > > that means when I generate the topology file by pdb2gmx I will add > manually > > the section [constraints] on it? > > I suggest you look into the manual to understand different ways of > applying constraints. You can either convert bonds into constraints via > the "constraints" .mdp option, in which case the force constants are > irrelevant but the equilibrium lengths matter, or you do not define any > bonds and manually write in the [constraints]. It depends on how you > need to treat the system. I know nothing about POMs so I can't comment > specifically. If the species is treated as a fully rigid entity (not > something GROMACS is really well suited for), then you should probably > be writing the topology manually because you will have lots of bonds to > non-sequential atoms. > > -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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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] Info regarding restrained minimization, equilibration & production
Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it? Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:50 Justin Lemkul ha scritto: > > > On 5/7/20 8:47 AM, Paolo Costa wrote: > > Dear Justin, > > > > I thought too. > > In case, could you please indicate me how I can constrain the interatomic > > distance of a desired molecule, in such case the POM molecule? > > Define [constraints] in the topology for all relevant interatomic > distances. > > -Justin > > > Thanks a lot. > > > > Paolo > > > > Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul > ha > > scritto: > > > >> > >> On 5/7/20 8:41 AM, Paolo Costa wrote: > >>> Dear Justin, > >>> > >>> thanks a lot for your valuable information. > >>> The system (Keggin anion, POM) I am trying to simulate is almost > >> identical > >>> to the one already studied in literature (doi: 10.1021/jp077098p). > >>> In the SI of this work, the authors stated "*Keggin anions are treated > as > >>> rigid particles thus keeping constant the distances between the > different > >>> metal and oxygen atom".* > >>> That means they did not parametrize the bonded interactions for such > >>> molecule, isn't? > >> That sounds to me like all interatomic distances were fixed via > >> constraints, but you should contact the corresponding author to be sure, > >> and ask for example inputs. > >> > >> -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. > >> > > > > -- > == > > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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] Info regarding restrained minimization, equilibration & production
On 5/7/20 8:53 AM, Paolo Costa wrote: Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it? I suggest you look into the manual to understand different ways of applying constraints. You can either convert bonds into constraints via the "constraints" .mdp option, in which case the force constants are irrelevant but the equilibrium lengths matter, or you do not define any bonds and manually write in the [constraints]. It depends on how you need to treat the system. I know nothing about POMs so I can't comment specifically. If the species is treated as a fully rigid entity (not something GROMACS is really well suited for), then you should probably be writing the topology manually because you will have lots of bonds to non-sequential atoms. -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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
On 5/7/20 8:47 AM, Paolo Costa wrote: Dear Justin, I thought too. In case, could you please indicate me how I can constrain the interatomic distance of a desired molecule, in such case the POM molecule? Define [constraints] in the topology for all relevant interatomic distances. -Justin Thanks a lot. Paolo Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul ha scritto: On 5/7/20 8:41 AM, Paolo Costa wrote: Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus keeping constant the distances between the different metal and oxygen atom".* That means they did not parametrize the bonded interactions for such molecule, isn't? That sounds to me like all interatomic distances were fixed via constraints, but you should contact the corresponding author to be sure, and ask for example inputs. -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. -- == 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Dear Justin, I thought too. In case, could you please indicate me how I can constrain the interatomic distance of a desired molecule, in such case the POM molecule? Thanks a lot. Paolo Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul ha scritto: > > > On 5/7/20 8:41 AM, Paolo Costa wrote: > > Dear Justin, > > > > thanks a lot for your valuable information. > > The system (Keggin anion, POM) I am trying to simulate is almost > identical > > to the one already studied in literature (doi: 10.1021/jp077098p). > > In the SI of this work, the authors stated "*Keggin anions are treated as > > rigid particles thus keeping constant the distances between the different > > metal and oxygen atom".* > > That means they did not parametrize the bonded interactions for such > > molecule, isn't? > > That sounds to me like all interatomic distances were fixed via > constraints, but you should contact the corresponding author to be sure, > and ask for example inputs. > > -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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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] Info regarding restrained minimization, equilibration & production
On 5/7/20 8:41 AM, Paolo Costa wrote: Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus keeping constant the distances between the different metal and oxygen atom".* That means they did not parametrize the bonded interactions for such molecule, isn't? That sounds to me like all interatomic distances were fixed via constraints, but you should contact the corresponding author to be sure, and ask for example inputs. -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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus keeping constant the distances between the different metal and oxygen atom".* That means they did not parametrize the bonded interactions for such molecule, isn't? Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:20 Justin Lemkul ha scritto: > > > On 5/6/20 11:35 AM, Paolo Costa wrote: > > Dear Gromacs users, > > > > I am interested on studying the interaction between large metal cluster > > anions (polyoxometallates, POM) with different organic cations (e.g > > perylenes, etc..) in water. > > I have already the non bonded parameters of POMs from literature, while > the > > bonded parameters I calculated from Gaussian and VFFDT software. > > If I do not apply a position restraining force on the POM atoms, the POM > > structure gets distorted too much from the experimental one. I guess this > > is due to the lack of a good force field parametrization for > > metal-containing compound. > > *Thus, my question is the following:* > > *can I keep applying a position restraining force on POM atoms during the > > minimization, equilibration and production steps or is it conceptually > > wrong?* > > If you're restraining a configuration because the force field is so bad, > I'd immediately be skeptical of the quality of any simulation. Bonded > parameters are generally easy to reproduce and probably aren't the > source of your problem if you've implemented them carefully, but if > you're trying to combine new bonded parameters with existing nonbonded > parameters, you need to do careful validation on a known system. > > If your system doesn't work, you should back up and make sure you can > reproduce a published study using the same parameters and not ones of > your creation. > > -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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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] Need help creating md.mdp for silica(quartz)?
Hello Justin, so I believe it's just pbc visualization stuff going on then.. okay.. yes you can do it then from trjconv . Regards, Debashish On Thu, 7 May 2020, 14:14 Debashish Banerjee, wrote: > Hello Ekatherina, I did not reach a point in my simulations where I have > used freeze command, but I think for your case, can't you put a position > constraint on your quartz layer. In that case, you just have to create an > index file having quartz in the group and then you can put postion > restraints on them in x,y,z by putting force constant of [1000 1000 1000] > so that the layer doesn't move. > > Regards, > Debashish > > > > > > On Thu, 7 May 2020, 10:28 Ekatherina O, wrote: > >> Hello Dr. Dallas Warren, >> Thank you for the suggestions. >> >> But this does not solve the problem of the movement of atoms of quartz >> layers (upper and lower) located at the borders of the box. I would like >> the quartz layers to remain intact during the modeling process, i.e. >> atoms did not move and the initial structure was disturbed. How can I >> solve this problem? >> Can I freeze structure (atoms)? Since with a further increase in >> simulation time, I observe the movement of quartz layers in the box. I >> don’t need them to move. >> >> > Message: 4 >> > Date: Tue, 5 May 2020 09:12:51 +1000 >> > From: Dallas Warren >> > To: GROMACS users >> > Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? >> > Message-ID: >> > > dtxkx86ohdbsdyjg2ma2+tpa8ge...@mail.gmail.com> >> > Content-Type: text/plain; charset="UTF-8" >> > >> > 1/ it means that between the original coordinate file loaded with vmd >> > and >> > the frame you are looking at there from the trajectory file, those >> > atoms >> > have moved across the periodic boundary and vmd is still drawing the >> > bond >> > between them. vmd knows nothing about bonds, it guesses where the bonds >> > should be and maintains them between those atoms when viewing a >> > trajectory. >> > If looking to make a nice looking animation simply using gmx trjconv to >> > move the layer into the center of the box. Otherwise use a viewing >> > method >> > in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws >> > each frame i.e. DynamicBonds >> > >> > 2/ where the simulation box is located is entirely arbitrary. So if it >> > is >> > not in the location you want then use gmx trjconv to move it to where >> > you >> > want it to be. >> > >> > All these things you are seeing here are artifacts of the periodic >> > boundary >> > condition: >> > >> http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc >> > >> > >> > 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. >> >> -- >> Yours sincerely, >> Ekatherina O. >> o...@isc-ras.ru >> -- >> 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] Info regarding restrained minimization, equilibration & production
On 5/6/20 11:35 AM, Paolo Costa wrote: Dear Gromacs users, I am interested on studying the interaction between large metal cluster anions (polyoxometallates, POM) with different organic cations (e.g perylenes, etc..) in water. I have already the non bonded parameters of POMs from literature, while the bonded parameters I calculated from Gaussian and VFFDT software. If I do not apply a position restraining force on the POM atoms, the POM structure gets distorted too much from the experimental one. I guess this is due to the lack of a good force field parametrization for metal-containing compound. *Thus, my question is the following:* *can I keep applying a position restraining force on POM atoms during the minimization, equilibration and production steps or is it conceptually wrong?* If you're restraining a configuration because the force field is so bad, I'd immediately be skeptical of the quality of any simulation. Bonded parameters are generally easy to reproduce and probably aren't the source of your problem if you've implemented them carefully, but if you're trying to combine new bonded parameters with existing nonbonded parameters, you need to do careful validation on a known system. If your system doesn't work, you should back up and make sure you can reproduce a published study using the same parameters and not ones of your creation. -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.
Re: [gmx-users] Question on energygrps setting
On 5/6/20 6:31 PM, Lei Qian wrote: Dear users, I know interaction energy calculation is carried out via energygrps setting in mdp file. Because free energy-related settings do not include this energygrps setting, so I think this energygrps setting may NOT be related to free energy settings. Could I ask whether my idea is correct or not? The two have nothing to do with one another. In general, energygrps shouldn't be used during an MD simulation anyway, and should be treated as an analysis method. -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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
On 5/7/20 4:24 AM, Ekatherina O wrote: Hello Dr. Dallas Warren, Thank you for the suggestions. But this does not solve the problem of the movement of atoms of quartz layers (upper and lower) located at the borders of the box. I would like the quartz layers to remain intact during the modeling process, i.e. atoms did not move and the initial structure was disturbed. How can I solve this problem? I will reiterate what Dallas has said - if you have atoms that are exactly at the bottom of the box, they effectively *are* the boundary and therefore can seem to "jump" back and forth. This has no implication whatsoever on the physics, just visualization. You can "fix" the issue after the fact with trjconv. Can I freeze structure (atoms)? Since with a further increase in simulation time, I observe the movement of quartz layers in the box. I don’t need them to move. Freezing is very artificial and leads to unphysical collisions. Avoid if at all possible. -Justin Message: 4 Date: Tue, 5 May 2020 09:12:51 +1000 From: Dallas Warren To: GROMACS users Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? Message-ID: Content-Type: text/plain; charset="UTF-8" 1/ it means that between the original coordinate file loaded with vmd and the frame you are looking at there from the trajectory file, those atoms have moved across the periodic boundary and vmd is still drawing the bond between them. vmd knows nothing about bonds, it guesses where the bonds should be and maintains them between those atoms when viewing a trajectory. If looking to make a nice looking animation simply using gmx trjconv to move the layer into the center of the box. Otherwise use a viewing method in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws each frame i.e. DynamicBonds 2/ where the simulation box is located is entirely arbitrary. So if it is not in the location you want then use gmx trjconv to move it to where you want it to be. All these things you are seeing here are artifacts of the periodic boundary condition: http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc 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. -- == 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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Hello Ekatherina, I did not reach a point in my simulations where I have used freeze command, but I think for your case, can't you put a position constraint on your quartz layer. In that case, you just have to create an index file having quartz in the group and then you can put postion restraints on them in x,y,z by putting force constant of [1000 1000 1000] so that the layer doesn't move. Regards, Debashish On Thu, 7 May 2020, 10:28 Ekatherina O, wrote: > Hello Dr. Dallas Warren, > Thank you for the suggestions. > > But this does not solve the problem of the movement of atoms of quartz > layers (upper and lower) located at the borders of the box. I would like > the quartz layers to remain intact during the modeling process, i.e. > atoms did not move and the initial structure was disturbed. How can I > solve this problem? > Can I freeze structure (atoms)? Since with a further increase in > simulation time, I observe the movement of quartz layers in the box. I > don’t need them to move. > > > Message: 4 > > Date: Tue, 5 May 2020 09:12:51 +1000 > > From: Dallas Warren > > To: GROMACS users > > Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? > > Message-ID: > >dtxkx86ohdbsdyjg2ma2+tpa8ge...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > 1/ it means that between the original coordinate file loaded with vmd > > and > > the frame you are looking at there from the trajectory file, those > > atoms > > have moved across the periodic boundary and vmd is still drawing the > > bond > > between them. vmd knows nothing about bonds, it guesses where the bonds > > should be and maintains them between those atoms when viewing a > > trajectory. > > If looking to make a nice looking animation simply using gmx trjconv to > > move the layer into the center of the box. Otherwise use a viewing > > method > > in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws > > each frame i.e. DynamicBonds > > > > 2/ where the simulation box is located is entirely arbitrary. So if it > > is > > not in the location you want then use gmx trjconv to move it to where > > you > > want it to be. > > > > All these things you are seeing here are artifacts of the periodic > > boundary > > condition: > > > http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc > > > > > > 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. > > -- > Yours sincerely, > Ekatherina O. > o...@isc-ras.ru > -- > 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
Many thanks Alex for your reply :) You have pressure scaling and LINCS convergence issues, suggesting that > the starting configuration is far from equilibrium, as well as > potentially other issues. > > How to check if my starting configuration is far from equilibrium ? I checked the Temperature and Pressure curves ( attached in the original email) and they look equilibirated. Is there anything I am missing? > 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. How can I make that my graphene edges are crystallographically commensurate with respect to PBC ? I have chosen box size equal to the graphene sheet size and increased the height to make sure that the deposited molecules will not be deposited out of my graphene sheet area. > Finally, make sure that the small molecules you're > depositing on graphene are properly pre-equilibrated. > > Actually, after your email, I did the simulation for both the graphene sheet and the deposited molecules (C60) each alone to check with one has problems with the lincs warning. The C60 alone was successfully completed. The Graphene sheet didn't work due to the lincs warning. I know now that the problem is only in the graphene sheet. > Alex > > Thanks, Mohamed > 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free volume variation during the simulation
Many thanks david for the explanation. In did NVT then NPT equilibiration and then the production run, in the production run .mdp file I have the same parameters as in NVT and NPT.mdp files. Does this mean that my simulation is a NVT simulation or NPT ? Is it possible to do only one of them (NVT or NPT) equilibiration ? I thought that I must do both of them before I start the final production run. Thanks again, Mohamed On Wed, May 6, 2020 at 12:50 PM David van der Spoel wrote: > Den 2020-05-06 kl. 10:21, skrev Mohamed Abdelaal: > > Yes I measured both, the density and the free volume using gromacs. > > > > Since the free volume changes with respect to time, shouldn’t the density > > also change with time ? > What do you mean with "changes"? If the density is constant (with > fluctuations) in an equilibrium NPT simulation then the free volume > should fluctuate around an average as well. > > If you have a NVT simulation on the other hand, the total density is > going to be constant, but if your system undergoes a phase change the > freevolume will change. > > > > Thanks, > > Mohamed > > > > On Wed, May 6, 2020 at 08:23 David van der Spoel > > wrote: > > > >> Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: > >>> Hello everybody, > >>> > >>> I have two fundamental questions please. > >>> > >>> I have measured the fee volume and I discovered that, the free volume > >>> changes with respect to the time during the production run (different > >> value > >>> for each frame). However I have measured the density but the result > does > >>> not change with respect to time. > >>> > >>> Shouldn't the density also changes with time if the free volume changes > >>> with time ? > >>> > >>> I also can't understand why the free volume changes with respect to the > >>> time, if the number of molecules and volume of box didn't change. > >>> > >>> Many Thanks, > >>> Mohamed > >>> > >> This is due to atomic fluctuations, that is they overlap more or less > >> depending on their distance, Did you use the freevolume tool in gromacs? > >> It may also depend on whether each freevolume calculations is converged > >> (-ninsert option). > >> > >> -- > >> David van der Spoel, Ph.D., > >> Professor of Biology > >> Uppsala University. > >> http://virtualchemistry.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. > >> > > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.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] Need help creating md.mdp for silica(quartz)?
Hello Dr. Dallas Warren, Thank you for the suggestions. But this does not solve the problem of the movement of atoms of quartz layers (upper and lower) located at the borders of the box. I would like the quartz layers to remain intact during the modeling process, i.e. atoms did not move and the initial structure was disturbed. How can I solve this problem? Can I freeze structure (atoms)? Since with a further increase in simulation time, I observe the movement of quartz layers in the box. I don’t need them to move. Message: 4 Date: Tue, 5 May 2020 09:12:51 +1000 From: Dallas Warren To: GROMACS users Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? Message-ID: Content-Type: text/plain; charset="UTF-8" 1/ it means that between the original coordinate file loaded with vmd and the frame you are looking at there from the trajectory file, those atoms have moved across the periodic boundary and vmd is still drawing the bond between them. vmd knows nothing about bonds, it guesses where the bonds should be and maintains them between those atoms when viewing a trajectory. If looking to make a nice looking animation simply using gmx trjconv to move the layer into the center of the box. Otherwise use a viewing method in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws each frame i.e. DynamicBonds 2/ where the simulation box is located is entirely arbitrary. So if it is not in the location you want then use gmx trjconv to move it to where you want it to be. All these things you are seeing here are artifacts of the periodic boundary condition: http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc 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. -- Yours sincerely, Ekatherina O. o...@isc-ras.ru -- 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.
