[gmx-users] Doubt from Graphene oxide layer
Hi, I want to create a Graphene Oxide (GO) layer using some computational tools. It consists of different type of functional groups like hydroxy, carboxylic, and epoxy. VMD can generate Graphene layer. How Can I generate GO layer by using some computational tools? Thanks -- Rakesh Pant/राकेश पंत Research Fellow/अनुसंधान फेलो Indian Institute of Science Education and Research (IISER) भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान Pune-411008, India/ पुणे - ४११००८, भारत Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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.org_gmx-users Digest, Vol 158, Issue 27
On Jun 5, 2017 4:50 AM, wrote: > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. RMSD Matrix error (Apramita Chand) >2. Re: EM error (?Mohammad Roostaie? ?) >3. Difference in properties when method of adding urea molecules > is changed in a simulation box (Apramita Chand) >4. Re: Difference in properties when method of adding urea > molecules is changed in a simulation box (Andr? Farias de Moura) >5. Re: Difference in properties when method of adding urea > molecules is changed in a simulation box (Mark Abraham) >6. Negative deuterium order parameters (Poncho Arvayo Zatarain) > > > -- > > Mess > > Message: 4 > Date: Sun, 4 Jun 2017 13:39:18 -0300 > F > > Hi Apramita, > > you have not told us how many urea molecules you have added to you system, > neither have you told how large your peptide of interest is, but usually > people studying denaturation of peptides use very concentrated urea > solutions (typically 8 M or so), which are highly viscous. > > If this is your case, 10 ns is certainly too short for equilibration and 20 > ns is also way too short for structural sampling, I would increase both by > maybe 5-10 fold longer if proper relaxation and sampling are expected (how > long is long enough can be monitored by the time evolution of the > properties of interest - only when plateaus are obtained you can begin the > production run) > > Andre > > > On Sun, Jun 4, 2017 at 12:39 PM, Apramita Chand > wrote: > > > Dear All, > > > > I have tested with two ways of solvating a peptide with urea-water mixture > > Method 1: Pre-equilibrating a urea-water box and solvating the peptide with > > -cs option with this box > > > > Method 2: Adding urea molecules to peptide box using -ci option and then > > solvating the resulting box with water molecules > > > > In both the methods, same number of urea and water molecules were added . > > 10ns equilibration followed by 20ns simulation steps were carried out. > > On analysing the properties, average number of hydrogen bonds between > > peptide-water in method 1 was 16.221 while it changed to 14.340 in Method > > 2. Similarly, number of H-bonds between peptide-urea changed from 5.687 to > > 4.031 on switching from Method 1 to Method 2. > > > > On checking radial distribution functions, interaction between > > water-peptide sites were somewhat similar for both Methods but significant > > changes were found for peptide-urea site-site correlations. Method-1 showed > > higher peptide-urea interaction. > > > > What could be the reason for these discrepancies? Are both methods correct? > > I want to go on with Method-2 for further simulations because it is > > relatively simpler but Method-1 shows higher hydrogen bonding between > > sites. > > > > Please suggest. > > > > yours sincerely, > > Apramita > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > _ > > Prof. Dr. Andr? Farias de Moura > Department of Chemistry > Federal University of S?o Carlos > S?o Carlos - Brazil > phone: +55-16-3351-8090 > > > -- > > Message: 5 > Date: Sun, 04 Jun 2017 17:10:29 + > From: Mark Abraham > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Difference in properties when method of > adding urea molecules is changed in a simulation box > Message-ID: > < camnumaqn3rggkta2jdsjugxltap_jma6w2n8pwgily4d-hw...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > Further, I would measure the distribution of the lifetime of hydrogen > bonds, since you need to sample much longer than eg the average. And you > should also try to measure the autocorrelation time of the number of > hydrogen bonds - you don't have a "new" observation until you've simulated > at least that long. Those will probably point to the fact that you aren't > comparing the long sampling time limit in either case. > > Mark > > On Sun, 4 Jun 2017 18:39 Andr? Farias de Moura wrote: > > > Hi Apramit
Re: [gmx-users] Doubt from Graphene oxide layer
First let us know what do you mean by some computational tools. If you really mean "some" then you vast choices like chem craft, accrlys draw, gauss view, chem draw, Marvin tools, These are user friendly and you have lot YouTube tutorials Can help for further classifications. On Mon, 5 Jun 2017 at 12:40 PM, Rakesh Pant < rakesh.p...@students.iiserpune.ac.in> wrote: > Hi, > > I want to create a Graphene Oxide (GO) layer using some computational > tools. It consists of different type of functional groups like hydroxy, > carboxylic, and epoxy. VMD can generate Graphene layer. How Can I generate > GO layer by using some computational tools? > > Thanks > > -- > Rakesh Pant/राकेश पंत > Research Fellow/अनुसंधान फेलो > Indian Institute of Science Education and Research (IISER) > भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान > Pune-411008, India/ पुणे - ४११००८, भारत > Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Fwd: Analysis
-- Forwarded message - From: RAHUL SURESH Date: Thu, 1 Jun 2017 at 7:05 PM Subject: Analysis To: I have few doubts in MD analysis. *How to calculate the deviation angle between two helix of a protein? (for every ns) or in other words how can I know whether the two helices (consecutive) have moved apart during simulation? *In saltbridge analysis how can I eliminate CL and NA ions? (Before the analysis) PS:- Its Protein-Ligand complex simulated for 100ns. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Analysis
Hi, On Thu, Jun 1, 2017 at 3:35 PM RAHUL SURESH wrote: > I have few doubts in MD analysis. > > *How to calculate the deviation angle between two helix of a protein? (for > every ns) or in other words how can I know whether the two helices > (consecutive) > have moved apart during simulation? > Various of the analysis tools may be helpful here. Start at http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html#commands-by-topic > *In saltbridge analysis how can I eliminate CL and NA ions? (Before the > analysis) > Probably through use of suitable index groups, which you probably learned about in tutorials or have seen in the documentation. Mark > PS:- Its Protein-Ligand complex simulated for 100ns. > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] Segmentation fault (core dumped) Too many LINCS warnings
Dear All I've been trying to create a DPPC bilayer with polarizable water for the past week, but I've gotten "Segmentation fault (core dumped)" error message every single time during the production run, and despite all my efforts, I haven't been able to figure out a solution for this error. My box is (7.5) nm cubed, and there are 128 DPPC molecules which I tried to solvate with 768 Polarizable Water beads. For shorter time period of ~5ns I get many LINCS warnings but I'm able to complete the run. For longer simulations ~20ns, I get too many LINCS warnings, and it gives the aforementioned error and the run crashes? I've looked into my .itp, .mdp files but just can't figure out what might be wrong. Any suggestions on how to solve this? -- *Thank You* *Deepes* *h Sigdel* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Significance of box vectors in GRO trajectory file.
Dear Gromacs Users, Suppose I have a trajectory file in gro format. If I change the last line for each snapshot (i.e. line with box vectors values) into an arbitrary set of three numbers, will it have impact on further manipulations of this gro trajectory file with trjconv? In other words, is the line with box vector significant for a following command: gmx trjconv -f npt-md2-system.gro -o npt-md2-0-0.5ns.gro -s npt-md2.tpr -ndec 6 -pbc mol -center ? I especially worry whether it is going to be fine for -pbc mol and -center options. Do they read this vector at all? Best wishes, Dawid -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Significance of box vectors in GRO trajectory file.
On 6/5/17 10:07 AM, Dawid das wrote: Dear Gromacs Users, Suppose I have a trajectory file in gro format. If I change the last line for each snapshot (i.e. line with box vectors values) into an arbitrary set of three numbers, will it have impact on further manipulations of this gro trajectory file with trjconv? In other words, is the line with box vector significant for a following command: gmx trjconv -f npt-md2-system.gro -o npt-md2-0-0.5ns.gro -s npt-md2.tpr -ndec 6 -pbc mol -center ? I especially worry whether it is going to be fine for -pbc mol and -center options. Do they read this vector at all? Yes, the box vectors are used for reimaging and if you change them you will change both the centering and re-wrapping of coordinates. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Significance of box vectors in GRO trajectory file.
By "rewraping coordinates" do you mean how molecules that went outside of the box are treated? By the way, why does this vector change during simulation? What if I use exactly the same vector for my whole simulation? Best wishes, Dawid 2017-06-05 16:08 GMT+02:00 Justin Lemkul : > > > On 6/5/17 10:07 AM, Dawid das wrote: > >> Dear Gromacs Users, >> >> Suppose I have a trajectory file in gro format. If I change the last line >> for each >> snapshot (i.e. line with box vectors values) into an arbitrary set of >> three >> numbers, >> will it have impact on further manipulations of this gro trajectory file >> with trjconv? >> >> In other words, is the line with box vector significant for a following >> command: >> >> gmx trjconv -f npt-md2-system.gro -o npt-md2-0-0.5ns.gro -s npt-md2.tpr >> -ndec 6 -pbc mol -center >> >> ? >> I especially worry whether it is going to be fine for -pbc mol and -center >> options. >> Do they read this vector at all? >> > > Yes, the box vectors are used for reimaging and if you change them you > will change both the centering and re-wrapping of coordinates. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Significance of box vectors in GRO trajectory file.
On 6/5/17 10:14 AM, Dawid das wrote: By "rewraping coordinates" do you mean how molecules that went outside of the box are treated? I mean you're changing the distance between periodic images after the simulation, which means whatever reimaging you are doing via trjconv is wrong relative to what actually happened during the simulation. By the way, why does this vector change during simulation? What if I use exactly the same vector for my whole simulation? This is the function of pressure coupling. If you keep the box vectors fixed, that is an NVT simulation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Generation of density curve for biphasic system
Dear GROMACS user, I am trying to get the profile of density at interface for water/dodecane biphasic system. First I have prepared my index file with the command below *gmx_mpi make_ndx -f confout.gro* and it will genetare index.ndx. Then I have tried the command for interface density *gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat* But it will not write density.dat file. How the density profile can be generated ? Is there any other command to execute ? I need help in this regards. With thanx and regards Devraj Das -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Significance of box vectors in GRO trajectory file.
By the way, why does this vector change during simulation? What if I use >> exactly the same vector for my whole >> simulation? >> >> > This is the function of pressure coupling. If you keep the box vectors > fixed, that is an NVT simulation. Aaaah, very well then. Thank you for explaining that! Best wishes, Dawid -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Generation of density curve for biphasic system
On 6/5/17 10:25 AM, Debraj Das wrote: Dear GROMACS user, I am trying to get the profile of density at interface for water/dodecane biphasic system. First I have prepared my index file with the command below *gmx_mpi make_ndx -f confout.gro* and it will genetare index.ndx. Then I have tried the command for interface density *gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat* But it will not write density.dat file. Why not? Do you get an error? How the density profile can be generated ? Is there any other command to execute ? I need help in this regards. gmx density is probably the easier option here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] System Charge
Hi all, My system has still got a non-zero total charge of 9 after adding the counter-ions. Do I need for it to be zero in order to run the simulation or is it fine? Akash -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] System Charge
Hi, Is that a suitable model of your simulation system? Why is it better than one with a different number of ions? Mark On Mon, 5 Jun 2017 20:22 Pandya, Akash wrote: > Hi all, > > My system has still got a non-zero total charge of 9 after adding the > counter-ions. Do I need for it to be zero in order to run the simulation or > is it fine? > > > Akash > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] System Charge
Hi, Well I have to add 50mM of NaCl to my system, so I specified that on the genion command with the flag -conc and also entered -neutral. But it still came up with a charge of 9.26 so I am not sure? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 05 June 2017 19:30 To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] System Charge Hi, Is that a suitable model of your simulation system? Why is it better than one with a different number of ions? Mark On Mon, 5 Jun 2017 20:22 Pandya, Akash wrote: > Hi all, > > My system has still got a non-zero total charge of 9 after adding the > counter-ions. Do I need for it to be zero in order to run the > simulation or is it fine? > > > Akash > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] System Charge
Hi, I'm not sure either, but perhaps you should look at the output of genion and see what it said it was doing. Mark On Mon, Jun 5, 2017 at 8:35 PM Pandya, Akash wrote: > Hi, > > Well I have to add 50mM of NaCl to my system, so I specified that on the > genion command with the flag -conc and also entered -neutral. But it still > came up with a charge of 9.26 so I am not sure? > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 05 June 2017 19:30 > To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] System Charge > > Hi, > > Is that a suitable model of your simulation system? Why is it better than > one with a different number of ions? > > Mark > > On Mon, 5 Jun 2017 20:22 Pandya, Akash wrote: > > > Hi all, > > > > My system has still got a non-zero total charge of 9 after adding the > > counter-ions. Do I need for it to be zero in order to run the > > simulation or is it fine? > > > > > > Akash > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)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] gmx trjconv -center -boxcenter zero isn't amazing at putting the selection at (0, 0, 0), but I don't know why
OK, now I know why it's centering (max-min)/2 and not the center of mass or center of geometry. I knew this 6 years ago but appear to have forgotten 😉 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-June/062239.html I'll hack the code in gmx_trjconv.c to get the behaviour I need. Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christopher Neale Sent: 01 June 2017 15:58:58 To: Discussion list for GROMACS users Subject: [gmx-users] gmx trjconv -center -boxcenter zero isn't amazing at putting the selection at (0, 0, 0), but I don't know why Dear Users: Using gmx 5.1.2, I find that centering a selection of the system at (0,0,0) works better via "editconf -c -center 0 0 0" than it does via "trjconv -center -boxcenter zero" here's the comparison of the center of mass of the selection centered in these two different ways: TRJCONV: 1000 -0.0356 -0.191707 -0.00163571 EDITCONF: 1000 0.00042 -1.42837e-05 0.000364283 And that was generated by this script: #!/bin/bash . ~/.gmx5.1.2 echo -e "r_2-26_r_40-56_r_69-166_AND_C-alpha\nSystem\n" | gmx trjconv -f fittedx.gro -s fittedx.gro -n angindex.ndx -o fitted_t.gro " echo -e "r_2-26_r_40-56_r_69-166_AND_C-alpha\nSystem\n" | gmx editconf -f fittedx.gro -n angindex.ndx -o fitted_e.gro -c -center 0 0 0 echo "r_2-26_r_40-56_r_69-166_AND_C-alpha" | gmx traj -f fitted_t.gro -s fitted_t.gro -n angindex.ndx -com -ox coord_t.xvg echo "r_2-26_r_40-56_r_69-166_AND_C-alpha" | gmx traj -f fitted_e.gro -s fitted_e.gro -n angindex.ndx -com -ox coord_e.xvg echo "TRJCONV:" tail -n 1 coord_t.xvg echo "" echo "EDITCONF:" tail -n 1 coord_e.xvg # I get exactly the same values with a double precision compilation of gmx used for all steps in the script. All atoms in the selection are protein c-alpha (and I checked the selection to be sure there was no strange junk in there) so it should not be an issue with mass weighting. If I change the box size of the input fittedx.gro to be huge, it doesn't affect either result. I get the same result with gmx 4.6.7 If I take the editconf-centered output .gro file and run it through trjconv centering then it gives the same results as shown above for trjconv centering at zero (the ones that are not quite right). If I make the box 100,100,100 (exactly) and then use trjconv -boxcenter rect it puts the center of mass at 49.964 49.808 49.904 -- so pretty much the same offsets from the intended value as I reported above for -boxcenter zero. I can reproduce the issue of trjconv doing a worse job at centering than editconf as long as I have >2 atoms in the centered selection, and that's true even when I use "System" as the selection to be centered for a .gro file with only 3 atoms (all of type CA). Can anyone see what I am missing? Thank you, Chris. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] long equilibration for HII phase
Dear Gromacs users, I am using Charmm36 in Gromacs for doing MD on HII phase. I use the recommended optimized parameters by Charmm-GUI for using Charmm36 in Gromacs, although I made the HII phase systems. all the systems are running without any problem with a time step of 1 fs. The systems seem to be equilibrated (they have been run for almost 45 ns with such time step). However, still, when I used a dt of 2 fs, it crashes and some water molecules jump away. What would you suggest for this situation? Shall I use 1fs for the rest or there is another trick? Cheers, Mohsen -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Parameters for gram-positive peptidoglycan
Dear users, I was wondering if anyone has worked with a gram-positive peptidoglycan structure using GROMACS. If anyone has, can you please tell me how to get the correct parameters (topology, charges, etc) for the structure or link me to anybody else who does or references to gram-positive peptidoglycan parameter? Your help is much appreciated. Ty. With thanks and regards, Farisha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] tMPI error
Hi All, I wanted to run energy minimization process by this command: gmx mdrun -v -deffnm em. But, I got this error: tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted I do not know what the problem exactly is. Can you please help me? Thanks,Mohammad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] RMSD analysis
Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG analysis of complex system with that of monomer? If yes which part of the monomer trajectory should be considered.? Thank you -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Generation of density curve for biphasic system
Dear Justin, I am getting error with gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat It will not write anything in that file. I have also tried gmx density , but it is giving the overall density profile not for the individual phase. With regards Arya Das On Mon, Jun 5, 2017 at 7:58 PM, Justin Lemkul wrote: > > > On 6/5/17 10:25 AM, Debraj Das wrote: > >> Dear GROMACS user, >> >> I am trying to get the profile of density at interface for water/dodecane >> biphasic system. >> >> First I have prepared my index file with the command below >> >> *gmx_mpi make_ndx -f confout.gro* and it will genetare index.ndx. >> >> Then I have tried the command for interface density >> >> >> *gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat* >> But it will not write density.dat file. >> >> > Why not? Do you get an error? > > How the density profile can be generated ? Is there any other command to >> execute ? I need help in this regards. >> >> > gmx density is probably the easier option here. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RMSD Matrix Error
Dear Mark, Thanks for your reply. I think you're right about the space needed for generating RMSD Matrix. I definitely was short of 160GB !! Further, you've talked about me using highly correlated frames and that a suitable sub-sampling might solve the problem. How would I know which frames to use? Message: 2 Date: Mon, 05 Jun 2017 01:37:37 + From: Mark Abraham To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] RMSD Matrix error Message-ID: Content-Type: text/plain; charset="UTF-8" Hi, *On Sun, Jun 4, 2017 at 4:08 PM Apramita Chand > wrote: > Dear All, > > When I'm trying to construct a RMSD matrix , using the command > g_rms -s protein_equili.gro -f protein_model1_ut.xtc -m > rmsd-matrix.xpm -tu ns > > I get the error: > Last frame 20 time 20.000 > > Building RMSD matrix, 21x21 elements > element 28982; time 2.90 Killed* > That matrix has 4x10^10 elements, each of which needs 4 bytes of memory. 1GB is about 1x10^9 bytes, so you'd need at least 160 GB of memory. The real issue is that you are probably using a large number of highly correlated frames, so even if you could form the full distance matrix, you would not learn any more than you would from a matrix formed from a suitable sub-sampling. *> I have given the reference structure to be the one prior to production run > and after equilibration step. I have also tried the command with .tpr file. > Same error! >* The problem doesn't change with the nature of the reference structure. Mark yours sincerely, Apramita -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)
Dear Andre, I added around 56 molecules of urea to 966 water. The peptide is just 6 residues and I just wanted to see its preferred conformations as well as hydrogen bonding. I will definitely try to extend the simulation to atleast 100ns. For the equilibration, I found that the temperature and pressure had converged to its desired values within 10ns. Why do we need to give longer equilbration times? Please advise. yours sincerely Apramita > Message: 4 > Date: Sun, 4 Jun 2017 13:39:18 -0300 > F > > Hi Apramita, > > you have not told us how many urea molecules you have added to you system, > neither have you told how large your peptide of interest is, but usually > people studying denaturation of peptides use very concentrated urea > solutions (typically 8 M or so), which are highly viscous. > > If this is your case, 10 ns is certainly too short for equilibration and 20 > ns is also way too short for structural sampling, I would increase both by > maybe 5-10 fold longer if proper relaxation and sampling are expected (how > long is long enough can be monitored by the time evolution of the > properties of interest - only when plateaus are obtained you can begin the > production run) > > Andre > > > On Sun, Jun 4, 2017 at 12:39 PM, Apramita Chand > wrote: > > > Dear All, > > *> > I have tested with two ways of solvating a peptide with urea-water mixture > > Method 1: Pre-equilibrating a urea-water box and solvating the peptide with > > -cs option with this box > > > > Method 2: Adding urea molecules to peptide box using -ci option and then > > solvating the resulting box with water molecules > > > > In both the methods, same number of urea and water molecules were added . > > 10ns equilibration followed by 20ns simulation steps were carried out. > > On analysing the properties, average number of hydrogen bonds between > > peptide-water in method 1 was 16.221 while it changed to 14.340 in Method > > 2. Similarly, number of H-bonds between peptide-urea changed from 5.687 to > > 4.031 on switching from Method 1 to Method 2. > > > > On checking radial distribution functions, interaction between > > water-peptide sites were somewhat similar for both Methods but significant > > changes were found for peptide-urea site-site correlations. Method-1 showed > > higher peptide-urea interaction. > > > > What could be the reason for these discrepancies? Are both methods correct? > > I want to go on with Method-2 for further simulations because it is > > relatively simpler but Method-1 shows higher hydrogen bonding between > > sites. > > > > Please suggest. > > > > yours sincerely, > > Apramita > > -- > > Gromacs Users mailing list* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
