Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Hello Justin Lemkul, Thank you for the suggestions. I understood and already tried using transforms with trjconv. The picture got better. -- Message: 4 Date: Thu, 7 May 2020 08:17:06 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed 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. -- 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.
Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Hello Debashish, Thank you for the suggestions. Could you tell us in more detail how (in which file) postion restraints on them in x, y, z should be written by putting force constant of [1000 1000 1000 Could you please advise the links where I can read about it? Message: 3 Date: Thu, 7 May 2020 14:14:41 +0200 From: Debashish Banerjee To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)? Message-ID: Content-Type: text/plain; charset="UTF-8" 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 -- 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.
[gmx-users] Lazaro Andres Monteserin Castanedo shared "gibbs-1_2.xpm" with you
Hi Nikhil, Lazaro Andres Monteserin Castanedo (lamonteserincastan...@gmail.com) invited you to view the file " gibbs-1_2.xpm " on Dropbox. View file[1] Enjoy! The Dropbox team [1]: https://www.dropbox.com/l/scl/AADRnq_Zod0PzsbuSrY9eQBYX4o2QtoeR9U -- 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] 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.
[gmx-users] Question on energygrps setting
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? Thanks! Lei -- 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] Info regarding restrained minimization, equilibration & production
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?* Thanks. Best regards, Paolo -- 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] Free volume variation during the simulation
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.
Re: [gmx-users] Free volume variation during the simulation
I started with NVT then NPT then md production run. Thanks, Kohamed On Wed, May 6, 2020 at 10:40 Arun Srikanth wrote: > Is it an NPT simulation or NVT simulation? > Arun > > On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal, > wrote: > > > 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 ? > > > > 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. > > > > > -- > > 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] Free volume variation during the simulation
Is it an NPT simulation or NVT simulation? Arun On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal, wrote: > 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 ? > > 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. > > > -- > 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
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 ? 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. > -- 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
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.
Re: [gmx-users] Free volume variation during the simulation
I am simulating Crystal System (C60 molecules) Thanks, Mohamed On Wed, May 6, 2020 at 1:22 AM Arun Srikanth wrote: > Are you simulating a crystal or amorphous system? > > Arun > > On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal > wrote: > > > 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 > > -- > > 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] Free volume variation during the simulation
Are you simulating a crystal or amorphous system? Arun On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal wrote: > 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 > -- > 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] Free volume variation during the simulation
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 -- 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?
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 "../ClayFF.ff/MMT_UC/UC3B.itp" > > #include "../ClayFF.ff/MMT_UC/UC3T.itp" > > > > ; Added the part of defining ions.itp which contains Cs atom and defined > > position restrain parameters > > > > > > > > > > *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include > > "posres_Cs.itp"#endif* > > #include "../charmm36.ff/spc.itp" > > > > #include "../charmm36.ff/organics/act.itp" > > > > [ system ] > > ; Name > > clay + Cs + acetate + water > > > > [ molecules ] > > ; Compound#mols > > UC21 > > UC11 > > UC3B 1 > > UC21 > > UC21 > > UC11 > > UC11 > > UC21 > > UC21 > > UC3T 1 > > UC11 > > UC21 > > UC21 > > UC3B 1 > > UC3T 1 > > UC21 > > UC21 > > UC11 > > UC3B 1 > > UC21 > > UC21 > > UC11 > > UC11 > > UC21 > > UC21 > > UC3T 1 > > UC11 > > UC21 > > UC21 > > UC3B 1 > > UC3T 1 > > UC2 1 > > Na 24 > > SOL 312 > > UC2 1 > > UC1 1 > > UC3B 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3T 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3B 1 > > UC3T 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC3B 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3T 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3B 1 > > UC3T 1 > > UC2 1 > > Na 24 > > SOL312 > > UC2 1 > > UC1 1 > > UC3B 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3T 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3B 1 > > UC3T 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC3B 1 > > UC2 1 > > UC2 1 > > UC1 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3T 1 > > UC1 1 > > UC2 1 > > UC2 1 > > UC3B 1 > > UC3T 1 > > UC2 1 > > Na 24 > > Cs 16 > > act 16 > > SOL6103 > > > > *Step 3* > > In my mdp file, I defined it as follows: > > *define = -DPOSRES_Cs* > > > > > > *The problem : * > > gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr > > > > Setting the LD random seed to 1967282441 > > Generated 83825 of the 83845 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 1 > > Generated 57459 of the 83845 1-4 parameter combinations > > > > ERROR 1 [file posres_Cs.itp, line 5]: > > Atom index (5790) in position_restraints out of bounds (1-1). > > This probably
Re: [gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?
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 "../ClayFF.ff/MMT_UC/UC3B.itp" #include "../ClayFF.ff/MMT_UC/UC3T.itp" ; Added the part of defining ions.itp which contains Cs atom and defined position restrain parameters *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include "posres_Cs.itp"#endif* #include "../charmm36.ff/spc.itp" #include "../charmm36.ff/organics/act.itp" [ system ] ; Name clay + Cs + acetate + water [ molecules ] ; Compound#mols UC21 UC11 UC3B 1 UC21 UC21 UC11 UC11 UC21 UC21 UC3T 1 UC11 UC21 UC21 UC3B 1 UC3T 1 UC21 UC21 UC11 UC3B 1 UC21 UC21 UC11 UC11 UC21 UC21 UC3T 1 UC11 UC21 UC21 UC3B 1 UC3T 1 UC2 1 Na 24 SOL 312 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 Na 24 SOL312 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 Na 24 Cs 16 act 16 SOL6103 *Step 3* In my mdp file, I defined it as follows: *define = -DPOSRES_Cs* *The problem : * gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr Setting the LD random seed to 1967282441 Generated 83825 of the 83845 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 57459 of the 83845 1-4 parameter combinations ERROR 1 [file posres_Cs.itp, line 5]: Atom index (5790) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. http://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-index-n-in-position-restraints-out-of-bounds Presumably your Cs+ topology defines the [moleculetype] as having one ion in it. Therefore, the only valid atom number in [position_restraints] is 1. The global atom numbering is meaningless in the context of position restraints (which are assigned at the topology level) as genrestr warns you (see the help description; if you're trying to restrain anything that isn't the first molecule, you can't use it). The solution is to define a new [moleculetype] for the Cs+ ion you want to restrain, and use [position_restraints] 1 1 0 0 1000 in its topology. -Justin --
Re: [gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?
Just a small rectification: *posres_Cs.itp* were created and used every time. I mistakenly wrote posre_Cs.itp while typing it here, my bad. Thanks, Debashish On Tue, May 5, 2020 at 11:54 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 "../ClayFF.ff/MMT_UC/UC3B.itp" > #include "../ClayFF.ff/MMT_UC/UC3T.itp" > > ; Added the part of defining ions.itp which contains Cs atom and defined > position restrain parameters > > > > > *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include > "posres_Cs.itp"#endif* > #include "../charmm36.ff/spc.itp" > > #include "../charmm36.ff/organics/act.itp" > > [ system ] > ; Name > clay + Cs + acetate + water > > [ molecules ] > ; Compound#mols > UC21 > UC11 > UC3B 1 > UC21 > UC21 > UC11 > UC11 > UC21 > UC21 > UC3T 1 > UC11 > UC21 > UC21 > UC3B 1 > UC3T 1 > UC21 > UC21 > UC11 > UC3B 1 > UC21 > UC21 > UC11 > UC11 > UC21 > UC21 > UC3T 1 > UC11 > UC21 > UC21 > UC3B 1 > UC3T 1 > UC2 1 > Na 24 > SOL 312 > UC2 1 > UC1 1 > UC3B 1 > UC2 1 > UC2 1 > UC1 1 > UC1 1 > UC2 1 > UC2 1 > UC3T 1 > UC1 1 > UC2 1 > UC2 1 > UC3B 1 > UC3T 1 > UC2 1 > UC2 1 > UC1 1 > UC3B 1 > UC2 1 > UC2 1 > UC1 1 > UC1 1 > UC2 1 > UC2 1 > UC3T 1 > UC1 1 > UC2 1 > UC2 1 > UC3B 1 > UC3T 1 > UC2 1 > Na 24 > SOL312 > UC2 1 > UC1 1 > UC3B 1 > UC2 1 > UC2 1 > UC1 1 > UC1 1 > UC2 1 > UC2 1 > UC3T 1 > UC1 1 > UC2 1 > UC2 1 > UC3B 1 > UC3T 1 > UC2 1 > UC2 1 > UC1 1 > UC3B 1 > UC2 1 > UC2 1 > UC1 1 > UC1 1 > UC2 1 > UC2 1 > UC3T 1 > UC1 1 > UC2 1 > UC2 1 > UC3B 1 > UC3T 1 > UC2 1 > Na 24 > Cs 16 > act 16 > SOL6103 > > *Step 3* > In my mdp file, I defined it as follows: > *define = -DPOSRES_Cs* > > > *The problem : * > gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr > > Setting the LD random seed to 1967282441 > Generated 83825 of the 83845 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 57459 of the 83845 1-4 parameter combinations > > ERROR 1 [file posres_Cs.itp, line 5]: > Atom index (5790) in position_restraints out of bounds (1-1). > This probably means that you have inserted topology section > "position_restraints" in a part belonging to a different molecule than > you intended to. > In that case move the "position_restraints" section to the right > molecule. > > There were 2 notes > --- > Program: gmx grompp, version 2016.4 > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1880) > >
[gmx-users] How to apply position restrain on selected atoms in .gro files in Gromacs?
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 "../ClayFF.ff/MMT_UC/UC3B.itp" #include "../ClayFF.ff/MMT_UC/UC3T.itp" ; Added the part of defining ions.itp which contains Cs atom and defined position restrain parameters *#include "../ClayFF.ff/ions.itp"#ifdef POSRES_Cs#include "posres_Cs.itp"#endif* #include "../charmm36.ff/spc.itp" #include "../charmm36.ff/organics/act.itp" [ system ] ; Name clay + Cs + acetate + water [ molecules ] ; Compound#mols UC21 UC11 UC3B 1 UC21 UC21 UC11 UC11 UC21 UC21 UC3T 1 UC11 UC21 UC21 UC3B 1 UC3T 1 UC21 UC21 UC11 UC3B 1 UC21 UC21 UC11 UC11 UC21 UC21 UC3T 1 UC11 UC21 UC21 UC3B 1 UC3T 1 UC2 1 Na 24 SOL 312 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 Na 24 SOL312 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 UC2 1 UC1 1 UC3B 1 UC2 1 UC2 1 UC1 1 UC1 1 UC2 1 UC2 1 UC3T 1 UC1 1 UC2 1 UC2 1 UC3B 1 UC3T 1 UC2 1 Na 24 Cs 16 act 16 SOL6103 *Step 3* In my mdp file, I defined it as follows: *define = -DPOSRES_Cs* *The problem : * gmx_mpi grompp -f npt.mdp -c em.gro -p topol.top -o npt.tpr Setting the LD random seed to 1967282441 Generated 83825 of the 83845 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 57459 of the 83845 1-4 parameter combinations ERROR 1 [file posres_Cs.itp, line 5]: Atom index (5790) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section "position_restraints" in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. There were 2 notes --- Program: gmx grompp, version 2016.4 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1880) Fatal error: There was 1 error in input file(s) Kindly help me fix it please. With lots of hope of finding an answer -- *Best Regards* *Debashish Banerjee* *Ph.D. 3rd year (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
Re: [gmx-users] [gmx users] Terminal amide hydrogens not included in H-bond analysis
On 5/5/20 12:12 PM, Neena Susan Eappen wrote: Thank you Sahil, I will try VMD plugin for H-bond analysis. Thank you Justin for your reply, it looks like gmx hbond considers only one N-H as donor when part of NH2 group. Please take a look at this file. This is what gmx hbond does by default, see gmx help hbond: -[no]merge (yes) H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF. This is a very different situation than claiming the NH2 group simply isn't accounted for. -Justin https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing Many thanks, Neena From: Neena Susan Eappen Sent: Tuesday, April 28, 2020 1:50 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx users] Terminal amide hydrogens not included in H-bond analysis Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? Many thanks, Neena -- == 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] apply protonation state CYS amino acid
On 5/4/20 11:46 PM, azadeh kordzadeh wrote: Hi Thank you very much for your answer to my former question I want to select CYSH state but we have this option for this amino acid. already I could determine especial state for his,lys,arg,asp by command -his but this command doesn't work for CYS Deprotonated (anionic) Cys is treated as a special residue by all force fields, usually something like CYM because it is not normally considered a titratable amino acid. Check the force field .rtp file and adjust the residue name accordingly. -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] about how to create angle.index with specific angles
On 5/2/20 3:12 PM, lazaro monteserin wrote: Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD in the file (*dangle.trr*) with the following command: *gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral* (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (*covar.ndx*) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis: *gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 1* 1 was the time in ps for the last frame of the simulation. 5) I runned covar: *gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc* 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors: *gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg* 7) Then I got the projection in 3D of the free energy landscape: *gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm* Note: I attached all the files in the dropbox link below https://www.dropbox.com/sh/wez43stnyv4ho31/AABQ3xwgUGf0CuMI_UF7MGsWa?dl=0 I can't access the Dropbox folder because you have given permission for the mailing list email to access it. Please either make it public or upload to a different service. The most relevant files are 2dproj_1_2.xvg and gibbs-1_2.xpm -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] [gmx users] Terminal amide hydrogens not included in H-bond analysis
Thank you Sahil, I will try VMD plugin for H-bond analysis. Thank you Justin for your reply, it looks like gmx hbond considers only one N-H as donor when part of NH2 group. Please take a look at this file. https://drive.google.com/file/d/1EgJPbHXNCo--VFOoy1YYolBx3XKBKpiH/view?usp=sharing Many thanks, Neena From: Neena Susan Eappen Sent: Tuesday, April 28, 2020 1:50 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx users] Terminal amide hydrogens not included in H-bond analysis Hello gromacs users, My peptide has an amide group at the C-terminus. Hydrogen bond analysis using gmx hbond does not take into account H-bond donors (NH2) from the amide group (Note: this NH2 is considered as a residue according to opls ff). What might be happening here? Many thanks, Neena -- 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] Size of Water Pools
Hi All, I am simulating systems with lipids, water and surfactants. I observed formation of water pools/water aggregates with different sizes in final frames. Now I want to measure size of these pools. What gromacs tool do you suggest me to use? I tried to do clustering first and thought calculating radius of gyration. However, clustering process takes ages to complete. Could you please help me to determine size of these water pools? Thank you. -- Best Regards Shan Jayasinghe -- 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
Hi, Have you tried reducing the timestep in mdp? Yes, I tried. But no hope. On Mon, May 4, 2020, 2:52 AM Naba https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>> 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* On Mon, 4 May, 2020, 02:51 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
[gmx-users] apply protonation state CYS amino acid
Hi Thank you very much for your answer to my former question I want to select CYSH state but we have this option for this amino acid. already I could determine especial state for his,lys,arg,asp by command -his but this command doesn't work for CYS 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] Need help creating md.mdp for silica(quartz)?
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. On Mon, 4 May 2020 at 22:08, Ekatherina O wrote: > I have done simulation water in nanopore based on quartz (I use model > ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is > a link to the pictures at the initial time (1.png) and in the modeling > process. > > https://drive.google.com/drive/folders/1GpIyx8___kQ3Zbe36wkSSINxgtKwIWsn?usp=sharing > ) > Its NVT simulation (see .mdp below) and neutral charge on surface (have > silanol groups), system is overall neutral. > 1) Did I choose the right settings? What do these atomic displacements > (lines in the pictures) mean? What restrictions should be imposed on the > system? > 2) In addition, I noticed that all the atoms of the quartz walls that > are in the vicinity of the box walls move from the upper wall to the > lower and lower to the upper. How can I avoid this when periodic > boundary conditions are imposed? Do I understand correctly that this > involves interaction between the quartz walls? > > integrator = md-vv > dt = 0.001; = 1 fs > nsteps = 50 ; = 100 ps > nstcomm = 1 > ; OUTPUT CONTROL OPTIONS > nstxout = 200 > nstvout = 200 > nstfout = 200 > nstlog = 200 > nstenergy = 200 > energygrps = System > cutoff-scheme= Verlet > ; NEIGHBORSEARCHING PARAMETERS > ;periodic-molecules = no > nstlist = 20 > ns_type = grid > pbc = xyz > rlist = 1.4 > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = PME ; fourierspacing ; pme-order > ; = PPPM ; fourierspacing > ; = Ewald; No parallel Ewald. > rcoulomb= 1.4 > rvdw= 1.4 > ; Ewald, PME, PPPM options > ;fourierspacing = 0.12 > ;fourier_nx = 0 ; 2 3 5 7 > ;fourier_ny = 0 > ;fourier_nz = 0 > ;pme_order = 6; 10 ; 8 ; default = 4 > optimize_fft= yes > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > Tcoupl = nose-hoover > tc-grps = System > tau_t = 0.5 > ref_t = 298 > ;Pcoupl = berendsen > pcoupltype = isotropic > tau_p = 0.1 > compressibility = 0.0008076 > ref_p = 800 > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = yes > gen_temp= 298 > gen_seed= 173529 > ; OPTIONS FOR BONDS > constraints = all-bonds > constraint-algorithm = lincs > > > And sorry if I missed similar topic in mailing list, but I couldn't find > anything similar. > > > -- > 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] Set up anti parallel membrane system for CompEL simulation
Hi Jochen, Thank you for the suggestions. Best, Zheng On Mon, May 4, 2020 at 5:24 PM Jochen Hub wrote: > > > Am 04.05.20 um 23:21 schrieb Jochen Hub: > > > > > > Am 04.05.20 um 21:33 schrieb Zheng Ruan: > >> Hi, > >> > >> I'm trying to setup an antiparallel membrane system for CompEL > >> simulation. > >> It is relatively straightforward to convert an existing single membrane > >> system to a parallel system by using > >> > >> # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro > >> > >> However, is there an easy way to invert one of the membrane protein > >> configurations along with the membrane, water and ions? > > > > You could try: > > > > gmx editconf -rotate 90 0 0 > > Sorry, I meant of course editconf -rotate 180 0 0 > > You probably have to combine this with an editconf -translate, together > with a manual extension of the box by 1-2 Angstroem to avoid overlapping > water molecules at the box edge. > > Jochen > > > > > Cheers, Jochen > > > >> > >> Thanks, > >> Zheng > >> > > > > -- > --- > Prof. Dr. Jochen Hub > Theoretical Biophysics Group > Department of Physics, Saarland University > Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany > Phone: +49 (0)681 302-2740 > https://biophys.uni-saarland.de/ > --- > -- > 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] Set up anti parallel membrane system for CompEL simulation
Am 04.05.20 um 23:21 schrieb Jochen Hub: Am 04.05.20 um 21:33 schrieb Zheng Ruan: Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro However, is there an easy way to invert one of the membrane protein configurations along with the membrane, water and ions? You could try: gmx editconf -rotate 90 0 0 Sorry, I meant of course editconf -rotate 180 0 0 You probably have to combine this with an editconf -translate, together with a manual extension of the box by 1-2 Angstroem to avoid overlapping water molecules at the box edge. Jochen Cheers, Jochen Thanks, Zheng -- --- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany Phone: +49 (0)681 302-2740 https://biophys.uni-saarland.de/ --- -- 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] Set up anti parallel membrane system for CompEL simulation
Am 04.05.20 um 21:33 schrieb Zheng Ruan: Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro However, is there an easy way to invert one of the membrane protein configurations along with the membrane, water and ions? You could try: gmx editconf -rotate 90 0 0 Cheers, Jochen Thanks, Zheng -- --- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123 Saarbruecken, Germany Phone: +49 (0)681 302-2740 https://biophys.uni-saarland.de/ --- -- 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] Set up anti parallel membrane system for CompEL simulation
Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro However, is there an easy way to invert one of the membrane protein configurations along with the membrane, water and ions? Thanks, Zheng -- 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] GROMACS mailing-list will move to a forum
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] Free energy calculation and Lincs warning
Dear Gromacs users I am doing free energy calculation of the protein-ligand system in gromacs 2020 in which I am annihilating ligand by removing charges and vdw interactions. During Vdw removal I am facing lincs warning and my system crashes by generating different pdb structures. I have tried to use constraints on all bonds and also reduced time step to 1fs but still getting same problem as below:- Overriding thread affinity set outside gmx mdrun WARNING: There are no atom pairs for dispersion correction starting mdrun 'GROtesk MACabre and Sinister in water' 100 steps, 1000.0 ps. Step 853159, time 853.159 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000569, max 0.041969 (between atoms 3430 and 3439) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3435 3437 38.00.1400 0.1415 0.1400 3437 3438 52.20.1080 0.1068 0.1080 3437 3439 39.00.1400 0.1402 0.1400 Step 853159, time 853.159 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000550, max 0.040414 (between atoms 3430 and 3439) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3435 3437 37.80.1400 0.1415 0.1400 3437 3438 51.90.1080 0.1070 0.1080 3437 3439 38.60.1400 0.1403 0.1400 Step 853160, time 853.16 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000833, max 0.054713 (between atoms 3437 and 3438) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3430 3439 30.50.1457 0.1428 0.1400 Please find the mdp file as below:- ; Run control integrator = sd ; stochastic leap-frog integrator dt = 0.001 nsteps = 100 ; 1 ns comm-mode = Linear; remove center of mass translation nstcomm = 100 ; frequency for center of mass motion removal ; Output control nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy= 5000 nstxout-compressed = 5000 ; Bond parameters continuation= yes ; formerly known as 'unconstrained-start' - useful for exact continuations and reruns constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; bonds to H are constrained lincs_iter = 1 ; accuracy of LINCS lincs-order = 6; Highest order in the expansion of the constraint coupling matrix ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 10 ns_type = grid rlist= 1.2 pbc = xyz ; 3-D PBC ; Periodic boundary conditions ; Electrostatics coulombtype = PME rcoulomb = 1.2 pme-order = 6; interpolation order for PME (default is 4) fourierspacing = 0.10 ; grid spacing for FFT ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb ewald_geometry = 3d ; Ewald sum is performed in all three dimensions ; van der Waals vdwtype = cutoff vdw-modifier = Potential-shift-Verlet verlet-buffer-tolerance = 0.005 rvdw = 1.2 rvdw-switch = 1.0 DispCorr = EnerPres ; apply long range dispersion corrections for Energy and Pressure ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc-grps = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 298.15 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman pcoupltype = isotropic; uniform scaling of box vectors tau_p = 2.0 ; time constant (ps) ref_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) ; velocities gen_vel = no ; Velocity generation is on (if gen_vel is 'yes', continuation should be 'no') gen_seed = -1 ; Use random seed gen_temp = 298.15 ; Free energy control stuff free_energy = yes init_lambda_state= 17 delta_lambda = 0 calc_lambda_neighbors=-1; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 coul_lambdas = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
[gmx-users] Need help creating md.mdp for silica(quartz)?
I have done simulation water in nanopore based on quartz (I use model ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is a link to the pictures at the initial time (1.png) and in the modeling process. https://drive.google.com/drive/folders/1GpIyx8___kQ3Zbe36wkSSINxgtKwIWsn?usp=sharing) Its NVT simulation (see .mdp below) and neutral charge on surface (have silanol groups), system is overall neutral. 1) Did I choose the right settings? What do these atomic displacements (lines in the pictures) mean? What restrictions should be imposed on the system? 2) In addition, I noticed that all the atoms of the quartz walls that are in the vicinity of the box walls move from the upper wall to the lower and lower to the upper. How can I avoid this when periodic boundary conditions are imposed? Do I understand correctly that this involves interaction between the quartz walls? integrator = md-vv dt = 0.001; = 1 fs nsteps = 50 ; = 100 ps nstcomm = 1 ; OUTPUT CONTROL OPTIONS nstxout = 200 nstvout = 200 nstfout = 200 nstlog = 200 nstenergy = 200 energygrps = System cutoff-scheme= Verlet ; NEIGHBORSEARCHING PARAMETERS ;periodic-molecules = no nstlist = 20 ns_type = grid pbc = xyz rlist = 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME ; fourierspacing ; pme-order ; = PPPM ; fourierspacing ; = Ewald; No parallel Ewald. rcoulomb= 1.4 rvdw= 1.4 ; Ewald, PME, PPPM options ;fourierspacing = 0.12 ;fourier_nx = 0 ; 2 3 5 7 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 6; 10 ; 8 ; default = 4 optimize_fft= yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = nose-hoover tc-grps = System tau_t = 0.5 ref_t = 298 ;Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.1 compressibility = 0.0008076 ref_p = 800 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp= 298 gen_seed= 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = lincs And sorry if I missed similar topic in mailing list, but I couldn't find anything similar. -- 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.
Re: [gmx-users] Plumed tutorial
Hi Dinesh and others, I see a few PLUMED tutorials available online, but I wanted to just let anyone know that if they have developed a PLUMED tutorial or are working to create a new one, please feel free to submit any high-quality tutorials to LiveCoMS Journal: https://www.livecomsjournal.org/ I am the Tutorials Lead Editor for LiveCoMS, and we are interested in creating a centralized place for all high-quality, peer-reviewed tutorials for molecular modeling software (either QM or MM). Please contact me if you are interested in submitting a tutorial to us. Thanks, Mala On Mon, May 4, 2020 at 5:37 AM Dinesh Kumar wrote: > Dear gmx users,I am trying to run a protein-ligand simulation using PLUMED > patch.I would like to know if there is a step-by-step tutorial that could > help run metadynamics simulations using PLUMED (like the Gromacs tutorials > already available) > > Dinesh Kumar > > -- > 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. > -- Mala L. Radhakrishnan Associate Professor of Chemistry Director, Biochemistry Program Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- 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] Plumed tutorial
Dear gmx users,I am trying to run a protein-ligand simulation using PLUMED patch.I would like to know if there is a step-by-step tutorial that could help run metadynamics simulations using PLUMED (like the Gromacs tutorials already available) Dinesh Kumar -- 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] dssp 3.1.4
Hi, Do check out gmx do_dssp -h and make sure your dssp binary is the right version, with executable permissions, in the right place (or alternatively the appropriate environment variable is set, so that do_dssp can find dssp) Mark On Fri, 1 May 2020 at 18:47, Iman Katouzian wrote: > Good day, > > I have recently downloaded the latest dssp version and with the mkdssp > executable file as I type chmod +x dssp and run this code : > gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg > -tu ns > > the process starts but no output is created after even 1 day > my Gormacs version is 2019.3 and even earlier versions of dssp does not > work and give me the same result. Till now I have tested this process on 3 > computers having GROMACS 2019.3 on them. > > Can someone help me with this issue? > Many thanks. > > -- > > *Iman Katouzian* > > *Ph.D.** candidate of Food Process Engineering* > > *Faculty of Food Science and Technology* > > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* > -- > 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] How to recover the corrupted .xtc file?
Dear users, I have a corrupted .xtc file. I can read only part of the whole frame in VMD. When I gmx check the .edr file, there is no problem with 5001 frames. However if I do gmx check the .xtc file, then I get only 2954 frames out of 50001 frames. I used Gromacs 2019.6 with CUDA on a single node. I saved only xtc, edr, gro, cpt and log files. In addition, I cannot SCP the file to another machine. By a bash script (with PBS pro), I have run the simulation until md1.part0020.xtc without any problem. Is there a way to recover the xtc file? The following is the output from gmx check. GROMACS: gmx check, version 2019.6 Executable: /data/cluster/apps/gromacs/2019.6/bin/gmx Data prefix: /data/cluster/apps/gromacs/2019.6 Working dir: /data/../trj Command line: gmx check -f md1.part0003.xtc Checking file md1.part0003.xtc Reading frame 0 time 110060.000 # Atoms 35936 Precision 0.001 (nm) Reading frame2000 time 130060.000 WARNING: Incomplete frame: nr 2954 time 139600 Item#frames Timestep (ps) Step 295410 Time 295410 Lambda 0 Coords295410 Velocities 0 Forces 0 Box 295410 ## edr file Command line: gmx check -e md1.part0003.edr Checking energy file md1.part0003.edr Opened md1.part0003.edr as single precision energy file frame: 5503 (index 0), t: 110060.000 Last energy frame read 5000 time 160060.000 Found 5001 frames with a timestep of 10 ps. -- 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] 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.
Re: [gmx-users] Warning: Short Bond pdb2gmx (Justin Lemkul) (Sadaf Rani)
Thank you very much, Justin, for your valuable feedback. Regards. Sadaf -- 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 in free energy calculation (FAISAL NABI)
Dear Gromacs users I am using amber99sb-ildn.ff force field for protein and I used GAFF for ligand parameterization. I tried different options e.g using constraint =all bonds as well as h-bonds. Reducing the time step to 1 fs but still, I could not solve the problem and get lincs warning production run as below:- Step 106202, time 212.404 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035343, max 2.112628 (between atoms 3770 and 3773) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 90.02.2392 0.1552 0.1080 3770 3771 90.00.1045 0.1696 0.1090 3770 3772 90.02.9369 0.1212 0.1090 3770 3773 90.00.1043 0.3393 0.1090 Wrote pdb files with previous and current coordinates Step 106202, time 212.404 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.035038, max 2.096736 (between atoms 3770 and 3773) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3437 3438 90.02.2392 0.1540 0.1080 3770 3771 90.00.1045 0.1689 0.1090 3770 3772 90.02.9369 0.1198 0.1090 3770 3773 90.00.1043 0.3375 0.1090 I would really appreciate your help in fixing this problem I am facing since long. Thanks. Sadaf -- 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] Lazaro Andres Monteserin Castanedo shared "dPCA" with you
Hi Nikhil, Lazaro Andres Monteserin Castanedo (lamonteserincastan...@gmail.com) invited you to edit the folder " dPCA " on Dropbox. Lazaro Andres said: "Dear Dr. Lemkul I used the following protocol to generate the (.xpm) filesI followed the protocol in gromacs website to do dihedral Principal Component Analysis1) Created an index file (dangle.ndx) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before.2) Then I extracted the sincos of the angles in the dangle.ndx from my MD in the file (dangle.trr) with the following commandgmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral(I had 21 angles so it used 14 sincos to represent the angles)3) Then I generated an index file (covar.ndx) with a list of numbers from 1 to 14 for trjconv.4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysisgmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 11 was the time in ps for the last frame of the simulation.5) I runned covargmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectorsgmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg7) Then I got the projection in 3D of the free energy landscapegmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpmI would appreciate any feedbackThank you in advance Dr. LemkulKindly,Lazaro" Go to folder[1] Enjoy! The Dropbox team [1]: https://www.dropbox.com/l/scl/AACmJPduzqbNRmC7scaafSZ0pkU9B-KtLvo -- 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] dPCA - Compartido desde Dropbox
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD in the file (*dangle.trr*) with the following command: *gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral* (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (*covar.ndx*) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis: *gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 1* 1 was the time in ps for the last frame of the simulation. 5) I runned covar: *gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc* 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors: *gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg* 7) Then I got the projection in 3D of the free energy landscape: *gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm* Note: I attached all the files in the dropbox link below https://www.dropbox.com/sh/t0atsemijjmfo6m/AADGwMfvaSGaJTUOlCu_Gazla?dl=0 I would appreciate any feedback Thank you in advance Dr. Lemkul 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] about how to create angle.index with specific angles
Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (*dangle.ndx*) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the dangle.ndx from my MD in the file (*dangle.trr*) with the following command: *gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.trr -type dihedral* (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (*covar.ndx*) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis: *gmx trjconv -f dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e 1* 1 was the time in ps for the last frame of the simulation. 5) I runned covar: *gmx covar -f dangle.trr -s resized.gro -n covar.ndx -ascii -xpm -nofit -nomwa -noref -nopbc* 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors: *gmx anaeig -v eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2 -2d 2dproj_1_2.xvg* 7) Then I got the projection in 3D of the free energy landscape: *gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm -ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm* Note: I attached all the files in the dropbox link below https://www.dropbox.com/sh/wez43stnyv4ho31/AABQ3xwgUGf0CuMI_UF7MGsWa?dl=0 I would appreciate any feedback Thank you in advance Dr. Lemkul Kindly, Lazaro On Sat, May 2, 2020 at 8:47 AM Justin Lemkul wrote: > > > On 4/30/20 2:07 PM, lazaro monteserin wrote: > > Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. > > > > Now I am having issues opening the (.xpm) files generated that contain > for > > example the gibbs energy landscape on the two first eigenvectors of the > > dPCA. > > > > If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o > gibbs-1_2.eps" > > it write this error: "Input error or input inconsistency: > > Invalid XPixMap" > > > > Do you know if I am missing something here? Do I have to install > something > > in my OS to be able to see .xpm images? > > The error is coming from xpm2ps which means there's something wrong with > the .xpm file itself but without seeing how you generated it (exact > command and description of how you prepared the input data file) and > perhaps the .xpm file itself (uploaded somewhere), it's impossible to > comment further. > > -Justin > > > Thanks in advance, > > > > Lazaro > > > > On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: > > > >> > >> On 4/29/20 7:11 PM, lazaro monteserin wrote: > >>> Dear Dr. Lemkul it could be possible use that angle.index with the > >> selected > >>> dihedrals written by hand as index file for gmx angle for dihedral > >>> Principal Component Analysis? > >> You can create index groups however you like for whatever analysis you > >> want to perform. > >> > >> -Justin > >> > >>>Kindly, > >>> Lazaro > >>> > >>> On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > >>> > On 4/29/20 5:01 PM, lazaro monteserin wrote: > > Dear gromacs users, > > > > Is there any way to tell gmx mk_angndx to create the index file with > > dihedral angles from a (.tpr) for specific atom numbers (atom level, > >> e.g > 1, > > 2, 3) from my molecule? > mk_angndx is designed for distributions of similar angles (e.g. > evaluating force field sampling). If you want to compute specific > angles, use make_ndx or simply write the index groups by hand. > > -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 > >>
[gmx-users] Failed make check
Hello all, I was trying to install GROMACS 2020.2 and encountered a failed test at make check (#43, mdrun). I pasted what I think is the pertinent snippet below and the full output is in the link: https://www.dropbox.com/s/nfq6yojjdslhxur/make_check.log?dl=0 The cmake incovation was: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on I have been using GROMACS 2020 on the machine with various GTX GPUs without issues. For what it's worth, when I re-ran make check for that version, it passed. Many thanks for your help in advance, Gregory [--] 1 test from OriresTest [ RUN ] OriresTest.OriresCanRun NOTE 1 [file /home/e5-1650/Downloads/gromacs-2020.2/build/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Setting the LD random seed to -949742347 Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' Number of degrees of freedom in T-Coupling group System is 518.00 NOTE 2 [file /home/e5-1650/Downloads/gromacs-2020.2/build/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 notes Reading file /home/e5-1650/Downloads/gromacs-2020.2/build/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020 (single precision) Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. --- Program: mdrun-test, version 2020 Source file: src/gromacs/listed_forces/orires.cpp (line 127) Fatal error: Found 10 copies of a molecule with orientation restrains while the current code only supports a single copy. If you want to ensemble average, run multiple copies of the system using the multi-sim feature of mdrun. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- 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] Redmine posting forbidden?
On 5/2/20 12:13 PM, Eugene Radchenko wrote: Hello, I wanted to report a bug using the Redmine site. Unfortunately, even after registering, the option to submit an issue is missing from the Issues page (where I expected it). While the “File a new issue” link from the main page to https://redmine.gromacs.org/projects/gromacs/issues/new results in Error 403 “You are not authorized to access this page”. Am I doing something wrong? We use GitLab now: https://gitlab.com/gromacs -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.
[gmx-users] Redmine posting forbidden?
Hello, I wanted to report a bug using the Redmine site. Unfortunately, even after registering, the option to submit an issue is missing from the Issues page (where I expected it). While the “File a new issue” link from the main page to https://redmine.gromacs.org/projects/gromacs/issues/new results in Error 403 “You are not authorized to access this page”. Am I doing something wrong? Thank you Eugene -- 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] disulfide bridges
Oh thank you so much, I did not know it was a reference value. Given a range of values might exist in one system I'm guessing minimization would be the only way to deal with such a situation. Best, Miro On Sat, May 2, 2020 at 9:53 PM Justin Lemkul wrote: > > > On 5/2/20 6:54 AM, Miro Astore wrote: > > Hi all, > > > > I'm trying to make a protein with a fair few disulfide bridges and I > > couldn't get it to work. I chose -ss yes and increased the minimum > distance > > in specbonds.dat but it doesn't seem to want to let me see all possible > > pariings. > > specbond.dat does not set minimum distances. It sets a reference value, > and a bond is only assigned if the distance in the coordinate file is > within 10% of that reference. So if you were, for example, to increase > the value from 0.2 nm (conventional) to 0.3 nm, you'll miss the > disulfides that should be formed because the new reference range is 0.27 > - 0.33 nm and anything between 0.18 - 0.22 nm will not be assigned a > disulfide linkage. > > > Any way I can nudge it in the right direction without performing a > > minimisation with restraints? > > Depends on the range of distances in your structure, but this is often > what you have to do. > > -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. > -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] Warning: Short Bond pdb2gmx (Justin Lemkul)
On 5/2/20 8:21 AM, Sadaf Rani wrote: Dear Justin I want to get the equilibrium value for bond, angle and dihedral restraints to use in free energy calculation as mentioned in:- https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467 Looking forward to your kind suggestions, please. You can compute all geometric properties from a simulation using gmx distance, gmx angle, etc. -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] Warning: Short Bond pdb2gmx (Justin Lemkul)
Dear Justin I want to get the equilibrium value for bond, angle and dihedral restraints to use in free energy calculation as mentioned in:- https://pubs.acs.org/doi/abs/10.1021/jacs.6b11467 Looking forward to your kind suggestions, please. Thanks. Sadaf -- 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] disulfide bridges
On 5/2/20 6:54 AM, Miro Astore wrote: Hi all, I'm trying to make a protein with a fair few disulfide bridges and I couldn't get it to work. I chose -ss yes and increased the minimum distance in specbonds.dat but it doesn't seem to want to let me see all possible pariings. specbond.dat does not set minimum distances. It sets a reference value, and a bond is only assigned if the distance in the coordinate file is within 10% of that reference. So if you were, for example, to increase the value from 0.2 nm (conventional) to 0.3 nm, you'll miss the disulfides that should be formed because the new reference range is 0.27 - 0.33 nm and anything between 0.18 - 0.22 nm will not be assigned a disulfide linkage. Any way I can nudge it in the right direction without performing a minimisation with restraints? Depends on the range of distances in your structure, but this is often what you have to do. -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] Warning: Short Bond pdb2gmx
On 5/1/20 2:41 PM, Sadaf Rani wrote: Dear Gromacs users I did 50ns MD simulation of a protein-ligand complex. From this trajectory, I extracted region of trajectory having stable rmsd and generated an average structure. I want to run this average structure to get an idea of setting some restraints. but when I do gmx pdb2gmx I get following warning:- Warning: Short Bond (9-10 = 0.042416 nm) Warning: Short Bond (9-11 = 0.0463433 nm) Warning: Short Bond (9-12 = 0.0452425 nm) Warning: Short Bond (13-14 = 0.0407501 nm) Warning: Short Bond (13-15 = 0.0425715 nm) Warning: Short Bond (13-16 = 0.0421154 nm) Warning: Short Bond (65-66 = 0.0418464 nm) Warning: Short Bond (65-67 = 0.0454554 nm) Warning: Short Bond (65-68 = 0.0438005 nm) Warning: Short Bond (103-105 = 0.0498706 nm) Warning: Short Bond (103-106 = 0.0482166 nm) Warning: Short Bond (161-162 = 0.0384303 nm) Warning: Short Bond (161-163 = 0.0395632 nm) Warning: Short Bond (161-164 = 0.0404804 nm) Warning: Short Bond (178-179 = 0.0379231 nm) Warning: Short Bond (178-180 = 0.0350074 nm) Warning: Short Bond (178-181 = 0.0367544 nm) Warning: Short Bond (195-197 = 0.0491068 nm) Warning: Short Bond (240-241 = 0.0410752 nm) Warning: Short Bond (240-242 = 0.0400188 nm) Warning: Short Bond (240-243 = 0.0389276 nm) Warning: Short Bond (244-245 = 0.0395354 nm) Warning: Short Bond (244-246 = 0.0394185 nm) Warning: Short Bond (244-247 = 0.0411173 nm) Warning: Short Bond (254-255 = 0.0496385 nm) Warning: Short Bond (254-256 = 0.0490917 nm) Warning: Short Bond (254-257 = 0.0487225 nm) Warning: Short Bond (320-321 = 0.0389006 nm) Warning: Short Bond (320-322 = 0.0354672 nm) Warning: Short Bond (320-323 = 0.0318275 nm) Warning: Short Bond (332-333 = 0.044048 nm) Warning: Short Bond (332-334 = 0.0431301 nm) Warning: Short Bond (332-335 = 0.0443143 nm) Warning: Short Bond (339-340 = 0.0436942 nm) Warning: Short Bond (339-341 = 0.044572 nm) Warning: Short Bond (339-342 = 0.0438389 nm) Warning: Short Bond (386-387 = 0.0485982 nm) Warning: Short Bond (386-388 = 0.0493432 nm) Warning: Short Bond (400-401 = 0.0365161 nm) Warning: Short Bond (400-402 = 0.043 nm) Warning: Short Bond (400-403 = 0.038517 nm) Warning: Short Bond (552-553 = 0.0489085 nm) Warning: Short Bond (552-554 = 0.0483887 nm) Warning: Short Bond (552-555 = 0.0498913 nm) Warning: Short Bond (556-557 = 0.0345456 nm) Warning: Short Bond (556-558 = 0.0396005 nm) Warning: Short Bond (556-559 = 0.0370519 nm) Warning: Short Bond (575-576 = 0.0458407 nm) Warning: Short Bond (575-577 = 0.0455252 nm) Warning: Short Bond (575-578 = 0.0448519 nm) Warning: Short Bond (664-665 = 0.0423401 nm) Warning: Short Bond (664-666 = 0.0390075 nm) Warning: Short Bond (664-667 = 0.0406177 nm) Warning: Short Bond (671-672 = 0.0369435 nm) Warning: Short Bond (671-673 = 0.0354056 nm) Warning: Short Bond (671-674 = 0.0373171 nm) Warning: Short Bond (725-726 = 0.0389842 nm) Warning: Short Bond (725-727 = 0.0393952 nm) I understand that the average structure is not necessarily anything physically meaningful but how I assume that it can give the equilibrium values to set the restraints. What kind of restraints are you trying to set? I need your help to figure out this warning, please. The warning indicates what you've already read about average structures - they are physically nonsensical. You can't start a simulation from an average structure because it is totally distorted and therefore of essentially no use for almost anything. -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] PBC after energy minimization
On 5/1/20 9:29 AM, John Whittaker wrote: Hi Mohamed, Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve this problem after the energy minimization but I don't have .xtc file to use it as I do at the end. How can I solve this problem after the energy minimization ? You're saying that your energy minimization does not produce a trajectory (a .trr or .xtc file)? If that's the case, you just have to instruct GROMACS to periodically write to a trajectory file using options in the .mdp file (namely, nstxout). Take a look at: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html Under the section "output control" you will find what you are looking for. "Trajectories" from energy minimization are generally unreadable as the interval of saved frames is uneven. During EM, a frame is only written when the energy goes down, which is not necessarily every possible frame. I also seem to recall that there is never XTC output from EM, even if requested, because it's rather pointless. Maybe that has changed. -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] about how to create angle.index with specific angles
On 4/30/20 2:07 PM, lazaro monteserin wrote: Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. Now I am having issues opening the (.xpm) files generated that contain for example the gibbs energy landscape on the two first eigenvectors of the dPCA. If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o gibbs-1_2.eps" it write this error: "Input error or input inconsistency: Invalid XPixMap" Do you know if I am missing something here? Do I have to install something in my OS to be able to see .xpm images? The error is coming from xpm2ps which means there's something wrong with the .xpm file itself but without seeing how you generated it (exact command and description of how you prepared the input data file) and perhaps the .xpm file itself (uploaded somewhere), it's impossible to comment further. -Justin Thanks in advance, Lazaro On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: On 4/29/20 7:11 PM, lazaro monteserin wrote: Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis? You can create index groups however you like for whatever analysis you want to perform. -Justin Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: On 4/29/20 5:01 PM, lazaro monteserin wrote: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, 2, 3) from my molecule? mk_angndx is designed for distributions of similar angles (e.g. evaluating force field sampling). If you want to compute specific angles, use make_ndx or simply write the index groups by hand. -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.
[gmx-users] disulfide bridges
Hi all, I'm trying to make a protein with a fair few disulfide bridges and I couldn't get it to work. I chose -ss yes and increased the minimum distance in specbonds.dat but it doesn't seem to want to let me see all possible pariings. Any way I can nudge it in the right direction without performing a minimisation with restraints? Best, Miro -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] Warning: Short Bond pdb2gmx
Dear Gromacs users I did 50ns MD simulation of a protein-ligand complex. From this trajectory, I extracted region of trajectory having stable rmsd and generated an average structure. I want to run this average structure to get an idea of setting some restraints. but when I do gmx pdb2gmx I get following warning:- Warning: Short Bond (9-10 = 0.042416 nm) Warning: Short Bond (9-11 = 0.0463433 nm) Warning: Short Bond (9-12 = 0.0452425 nm) Warning: Short Bond (13-14 = 0.0407501 nm) Warning: Short Bond (13-15 = 0.0425715 nm) Warning: Short Bond (13-16 = 0.0421154 nm) Warning: Short Bond (65-66 = 0.0418464 nm) Warning: Short Bond (65-67 = 0.0454554 nm) Warning: Short Bond (65-68 = 0.0438005 nm) Warning: Short Bond (103-105 = 0.0498706 nm) Warning: Short Bond (103-106 = 0.0482166 nm) Warning: Short Bond (161-162 = 0.0384303 nm) Warning: Short Bond (161-163 = 0.0395632 nm) Warning: Short Bond (161-164 = 0.0404804 nm) Warning: Short Bond (178-179 = 0.0379231 nm) Warning: Short Bond (178-180 = 0.0350074 nm) Warning: Short Bond (178-181 = 0.0367544 nm) Warning: Short Bond (195-197 = 0.0491068 nm) Warning: Short Bond (240-241 = 0.0410752 nm) Warning: Short Bond (240-242 = 0.0400188 nm) Warning: Short Bond (240-243 = 0.0389276 nm) Warning: Short Bond (244-245 = 0.0395354 nm) Warning: Short Bond (244-246 = 0.0394185 nm) Warning: Short Bond (244-247 = 0.0411173 nm) Warning: Short Bond (254-255 = 0.0496385 nm) Warning: Short Bond (254-256 = 0.0490917 nm) Warning: Short Bond (254-257 = 0.0487225 nm) Warning: Short Bond (320-321 = 0.0389006 nm) Warning: Short Bond (320-322 = 0.0354672 nm) Warning: Short Bond (320-323 = 0.0318275 nm) Warning: Short Bond (332-333 = 0.044048 nm) Warning: Short Bond (332-334 = 0.0431301 nm) Warning: Short Bond (332-335 = 0.0443143 nm) Warning: Short Bond (339-340 = 0.0436942 nm) Warning: Short Bond (339-341 = 0.044572 nm) Warning: Short Bond (339-342 = 0.0438389 nm) Warning: Short Bond (386-387 = 0.0485982 nm) Warning: Short Bond (386-388 = 0.0493432 nm) Warning: Short Bond (400-401 = 0.0365161 nm) Warning: Short Bond (400-402 = 0.043 nm) Warning: Short Bond (400-403 = 0.038517 nm) Warning: Short Bond (552-553 = 0.0489085 nm) Warning: Short Bond (552-554 = 0.0483887 nm) Warning: Short Bond (552-555 = 0.0498913 nm) Warning: Short Bond (556-557 = 0.0345456 nm) Warning: Short Bond (556-558 = 0.0396005 nm) Warning: Short Bond (556-559 = 0.0370519 nm) Warning: Short Bond (575-576 = 0.0458407 nm) Warning: Short Bond (575-577 = 0.0455252 nm) Warning: Short Bond (575-578 = 0.0448519 nm) Warning: Short Bond (664-665 = 0.0423401 nm) Warning: Short Bond (664-666 = 0.0390075 nm) Warning: Short Bond (664-667 = 0.0406177 nm) Warning: Short Bond (671-672 = 0.0369435 nm) Warning: Short Bond (671-673 = 0.0354056 nm) Warning: Short Bond (671-674 = 0.0373171 nm) Warning: Short Bond (725-726 = 0.0389842 nm) Warning: Short Bond (725-727 = 0.0393952 nm) I understand that the average structure is not necessarily anything physically meaningful but how I assume that it can give the equilibrium values to set the restraints. I need your help to figure out this warning, please. Thanks in advance. Sadaf -- 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] dssp 3.1.4
Good day, I have recently downloaded the latest dssp version and with the mkdssp executable file as I type chmod +x dssp and run this code : gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg -tu ns the process starts but no output is created after even 1 day my Gormacs version is 2019.3 and even earlier versions of dssp does not work and give me the same result. Till now I have tested this process on 3 computers having GROMACS 2019.3 on them. Can someone help me with this issue? Many thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- 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] PBC after energy minimization
Hi Mohamed, > Hello everybody, > > In order to solve the PBC at the end I use the command: > > *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * > > followed by: > > *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* > > > I want to solve this problem after the energy minimization but I don't > have > .xtc file to use it as I do at the end. > > How can I solve this problem after the energy minimization ? You're saying that your energy minimization does not produce a trajectory (a .trr or .xtc file)? If that's the case, you just have to instruct GROMACS to periodically write to a trajectory file using options in the .mdp file (namely, nstxout). Take a look at: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html Under the section "output control" you will find what you are looking for. - John > > 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. > John Whittaker Ph.D. Candidate Department of Mathematics and Computer Science Freie Universität Berlin +49 0160 936 04221 -- 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] conformation tensor
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.
[gmx-users] PBC after energy minimization
Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve this problem after the energy minimization but I don't have .xtc file to use it as I do at the end. How can I solve this problem after the energy minimization ? 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] about how to create angle.index with specific angles
Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. Now I am having issues opening the (.xpm) files generated that contain for example the gibbs energy landscape on the two first eigenvectors of the dPCA. If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o gibbs-1_2.eps" it write this error: "Input error or input inconsistency: Invalid XPixMap" Do you know if I am missing something here? Do I have to install something in my OS to be able to see .xpm images? Thanks in advance, Lazaro On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul wrote: > > > On 4/29/20 7:11 PM, lazaro monteserin wrote: > > Dear Dr. Lemkul it could be possible use that angle.index with the > selected > > dihedrals written by hand as index file for gmx angle for dihedral > > Principal Component Analysis? > > You can create index groups however you like for whatever analysis you > want to perform. > > -Justin > > > Kindly, > > Lazaro > > > > On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > > > >> > >> On 4/29/20 5:01 PM, lazaro monteserin wrote: > >>> Dear gromacs users, > >>> > >>> Is there any way to tell gmx mk_angndx to create the index file with > >>> dihedral angles from a (.tpr) for specific atom numbers (atom level, > e.g > >> 1, > >>> 2, 3) from my molecule? > >> mk_angndx is designed for distributions of similar angles (e.g. > >> evaluating force field sampling). If you want to compute specific > >> angles, use make_ndx or simply write the index groups by hand. > >> > >> -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.
[gmx-users] GROMACS 2020.2 patch release available
Hi GROMACS users, The official release of GROMACS 2020.2 is available! This second patch release again fixes issues found since the initial release of GROMACS 2020 and the release of 2020.1. We encourage all users of the 2020 series to update to 2020.2. Please see the link to the release notes below for more details. You can find the code, documentation, release notes, and test suite at the links below. Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz Documentation: http://manual.gromacs.org/2020.2/index.html (including release notes, install guide, user guide, reference manual) Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.2.tar.gz Happy simulating! 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.
Re: [gmx-users] Invalid atomtype format (Justin Lemkul
On 4/30/20 7:10 AM, Sadaf Rani wrote: Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:- https://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 There's a lot to go through here with multiple ligands so I'm not going to be able to go through your files line-by-line. You have duplicate bond entries somewhere. Make your system simpler. Run *only* one ligand at a time through pdb2gmx to figure out which one is triggering the problem. Also note that you should remove the extraneous number 1 from all your [ bonds ] lines in your .rtp entries. They're going to lead to incorrect format in the resulting topology. Just specify the pairs of atoms that are bonded. -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] Invalid atomtype format (Justin Lemkul
Dear Justin I have removed the blank lines but getting a new warning while doing gmx pdb2gmx:- WARNING: Duplicate line found in or between hackblock and rtp entries I am not getting what else is wrong. Could you please help me to figure out. I have shared the file on the following link:- https://www.dropbox.com/s/c6tg9q4i0ara3vu/atomtypes.atp?dl=0 Thanks. Sadaf -- 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] Invalid atomtype format (Justin Lemkul)
On 4/29/20 7:41 PM, Sadaf Rani wrote: Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Remove the blank lines from the end of atomtypes.atp and it works fine. Note that you should not be including LJ parameters in atomtypes.atp. Those are for ffnonbonded.itp. The atomtypes.atp file needs only the atom type and its mass as it is only used by pdb2gmx. -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] about how to create angle.index with specific angles
On 4/29/20 7:11 PM, lazaro monteserin wrote: Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis? You can create index groups however you like for whatever analysis you want to perform. -Justin Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: On 4/29/20 5:01 PM, lazaro monteserin wrote: Dear gromacs users, Is there any way to tell gmx mk_angndx to create the index file with dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g 1, 2, 3) from my molecule? mk_angndx is designed for distributions of similar angles (e.g. evaluating force field sampling). If you want to compute specific angles, use make_ndx or simply write the index groups by hand. -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] Invalid atomtype format (Justin Lemkul)
Dear Justin I have shared the files for the users mailing list on the following link. https://www.dropbox.com/s/bfaq8z8iqojdm0r/Atom_type_error%20files.zip?dl=0 Thanks and Regards. Sadaf -- 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] about how to create angle.index with specific angles
Dear Dr. Lemkul it could be possible use that angle.index with the selected dihedrals written by hand as index file for gmx angle for dihedral Principal Component Analysis? Kindly, Lazaro On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul wrote: > > > On 4/29/20 5:01 PM, lazaro monteserin wrote: > > Dear gromacs users, > > > > Is there any way to tell gmx mk_angndx to create the index file with > > dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g > 1, > > 2, 3) from my molecule? > > mk_angndx is designed for distributions of similar angles (e.g. > evaluating force field sampling). If you want to compute specific > angles, use make_ndx or simply write the index groups by hand. > > -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.
