Re: [gmx-users] REMD Showing Zero Exchange Probability
Sorry for the delay..Thank you Mark.. On Sat, Jul 21, 2018 at 2:09 AM, Mark Abraham wrote: > Hi, > > You can't arbitrarily choose both the temperature range and number of > replicas and get non-zero exchange probability. See > https://pubs.acs.org/action/showCitFormats?doi=10.1021%2Fct800016r. For a > given average exchange probability, choose a range and thus the number of > replicas, or the number of replicas and thus the range. > > Mark > > On Fri, Jul 20, 2018, 10:39 Ligesh Lichu wrote: > > > Dear all, > > I have performed REMD for a system containing Protein, Reline, Urea > and > > Water in the temperature range 290 to 450 K consist of 16 replicas out of > > 47 replicas generated by REMD temperature generator. But after the MD > > simulation the exchange probability is zero. I have used position > > restraints for reline, urea and protein. Is there any chance that > position > > restraints cause the exchange probability to be zero? I have one more > > query that, the REMD temperature generator produced around 45 to 54 > > replicas for my system in the required temperature range. But I have only > > 80 processors to do the job, So is it necessary to choose the consecutive > > temperature replicas given by the REMD temperature generator or I can > skip > > some temperatures in between? > > > > If I am using the equation *Ti = T0 exp (k* i)*, what determines the > value > > of 'k' how it affects the exchange probability? How can I choose the > value > > of 'k' for an arbitrary system? > > > > Thanks in advance... > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)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] gromacs.org_gmx-users Digest, Vol 171, Issue 84
Hi! I gave these commands: gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr time -p mpirun gmx_mpi mdrun -v -deffnm md I kept md.mdp identical to the one given in the tutorial, except that I changed the number of steps to 2500. I got an error saying that 'topol' was inaccessible. The previous steps had gone smoothly, though. Looking forward to your kind help! Regards, Raag On Sun, Jul 22, 2018 at 3:30 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> 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. Re: Time series of the number of atoms with the volume > (Mark Abraham) >2. Re: (no subject) (pbusc...@q.com) >3. Re: topol file inaccessible (Quyen V. Vu) >4. Re: Tilt in the Bilayer (atb files) >5. tutorial problem (??131 ???) > > > -- > > Message: 1 > Date: Sat, 21 Jul 2018 19:56:07 +0200 > From: Mark Abraham > To: gmx-us...@gromacs.org > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: Re: [gmx-users] Time series of the number of atoms with the > volume > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > There's quite a few examples in its documentation, do look there for ideas. > You will need to decide some geometric criterion to define the volume of > the pore. > > Mark > > On Sat, Jul 21, 2018, 16:27 Mijiddorj B wrote: > > > Dear GMX users, > > > > I would like to make analysis of atom numbers within the certain volume > > such as pore of channel. If you have any experience, please advise me. > > How can I use gmx select for this purpose? > > > > Best regards, > > Miji > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Message: 2 > Date: Sat, 21 Jul 2018 16:57:46 -0500 > From: pbusc...@q.com > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] (no subject) > Message-ID: <24d089eb-46c3-460d-9f55-7737d219c...@q.com> > Content-Type: text/plain; charset=us-ascii > > Have you tried the "insert-chemicals-after-md" command ? > > PB > > > On Jul 11, 2018, at 4:50 AM, Mark Abraham > wrote: > > > > Hi, > > > > Are you trying to observe something about the transition, or merely the > > different end points? > > > > Mark > > > >> On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar > wrote: > >> > >> Dear all, > >> I am planning to do a simulation where after 50ns of simulation I want > to > >> add some other chemicals in the system and continue it for another > 50ns, so > >> that I can have the effect of that chemicals exclusively before and > after > >> adding it to the system.Is it at all possible? If yes please tell me the > >> protocol/ commands or give me some references where this type of > simulation > >> is used. Thanks in advance. > >> -Soham > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)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. > > > > -- > > Message: 3 > Date: Sun, 22 Jul 2018 08:56:18 +0700 > From: "Quyen V. Vu" > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] topol file inaccessible > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > you should provide here more information than that > > On Sat, Jul 21, 2018 at 11:42 PM, Ali Ahmed wrote: > > > hi >
[gmx-users] Replicating the Results from gmx covar
Hi, I've been developing codes to perform PCA of the alpha-carbons from a processed GROMACS trajectory of a protein in the human-readable .g96 format. I perform the standard post-processing of the trajectory (still in the compressed .xtc version generated from gmx mdrun) as follows: 1) I correct any broken bonds across the periodic boundary conditions (PBCs) using gmx trjconv and simultaneously move the centre-of-mass to the origin of the box using -center -boxcenter zero and output my reference structure used for the rest of the processing workflow, ref.pdb: echo "3 1" | gmx trjconv -f traj.xtc -s top.tpr -pbc whole -center -boxcenter zero -dump 0 -o ref.pdb where traj.xtc is the 'raw' trajectory output from mdrun and top.tpr is the topology generated by gmx grompp called immediately prior to the mdrun command that generates traj.xtc. 2) I remove any bonds broken across the PBCs in the trajectory using -pbc whole. In the same step, I set the center-of-mass of the protein to the origin of the simulation box using the command -center -boxcenter zero: echo "3 1" | gmx trjconv -f traj.xtc -s ref.pdb -pbc whole -center -boxcenter zero -o after_pbc.xtc 3) I remove the rotations in the trajectory by fitting to the reference structure in ref.pdb: echo "3 1" | gmx trjconv -quiet -f after_pbc.xtc -s ref.pdb -fit rot -o after_rot.xtc 4) I convert the trajectory to .g96 format for analysis: echo "3" | gmx trjconv -quiet -f after_rot.xtc -s $top -o traj.g96 keeping only the alpha-carbons. Then, I run my analysis codes on the traj.g96 file. One thing I calculate is the average structure and write it to a PDB file. Then, to benchmark my calculations, I compare my results to what GROMACS finds for a PCA of the alpha-carbons of the same input trajectory (without the processing steps given above): echo "3 3" | gmx covar -f traj.xtc -s top.tpr -ascii Now, things get sticky when I compare my PCA results to those found using GROMACS. The eigenvalues of the covaraince matrix that I get are nearly identically to what GROMACS finds, viz, for the first ten eigenvalues: Me: 1 0.19775810587712664 2 7.9646496095133204E-002 3 4.5068418039738017E-002 4 2.3479149896592204E-002 5 1.3160235463867121E-002 6 1.1623284734275811E-002 7 9.3204844796344801E-003 8 7.6473789980896715E-003 9 6.9955131377012871E-003 10 6.2603369172376079E-003 gmx covar: 1 0.197767 2 0.0796882 3 0.0450706 4 0.0234754 5 0.0131577 6 0.011621 7 0.0093207 8 0.0076525 9 0.00699542 10 0.00626022 But, the covariance matrices are subtly different, and different enough that it significantly effects the subsequent calculations using the covariance matrix. Furthermore, I find that the average structures are significantly different; the average from gmx covar appears to be rotated relative to the average structure I find using my code. Checking the reference structure, it looks as though the average I find is oriented roughly in line with the reference, but the average structure from gmx covar is rotated in a way I don't understand. I've done some seriously diagnostics on the code I wrote and checked all the obviously things ( is the covariance matrix symmetric? Are its eigenvectors orthogonal? Is the sum of the eigenvectors equal to the trace of the covariance matrix? Do I have six zero eigenvalues?, etc.) and everything passes. So, I'm led to conclude that I am processing the trajectory differently than what GROMACS is doing in the gmx covar function. To the best of my knowledge, given my relative lack of knowledge of C and C++ that when gmx covar fits to the reference structure and calculates averages, it 1) Removes broken bonds across PBCs in the reference structure and moves it the origin of the simulation box, and 2) Removes broken bonds across PBCs in the trajectory, moves the center-of-mass of the protein to the origin, then performs a rotational fit to the reference structure. But, it seems like that is what I am doing! My question (finally!) is 1) Is my interpretation of how GROMACS treats the trajectory inside gmx covar correct? If not, what is it doing? 2) Is it possible to reproduce the corrections GROMACS is making to the input trajectory in gmx covar using the tools in gmx trjconv? If not, is there any way to extract the corrected trajectory gmx covar is using to calculate the covariance matrix? Thanks, Eric Beyerle -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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 density -d Z in a system with pbc = xy
I have pbc only in X-Y directions in my simulations (pbc = xy), and I want to calculate the number density in Z direction using the "gmx density -f *.xtc -s *.tpr -d Z -dens number" but the gmx density just stuck in the beginning. I wonder how I can density in Z direction in such situations? Thank you. Best regards, 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.
Re: [gmx-users] question
Andrew, you do realize that defects in CNTs make them toxic to living organisms, right? That aside, the presence of water inside CNTs depends on their diameter and chirality, so it's kind of hard to tell. But if your setup is reasonable and you see water getting inside CNTs, that's your answer: water will reside inside CNTs. :) Alex On 7/24/2018 4:51 AM, Andrew Bostick wrote: Dear Mark and Alex, I want to use CNTs as drug carrier. I think I should consider water molecules inside the CNT. Do I think right? Best, AB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] unusual trajectory
I said other things as well, i.e. you could have issues with setup. Noone knows if your trajectory is "appropriate" and noone knows if your setup is correct. Could you upload your trajectory somewhere and tell everyone what you think is wrong? Also, I recall both Justin and myself telling you to use appropriate box size in the CNT's axial direction. Did you do that? Also, what is your forcefield? Why are you using short (0.9 nm) cutoffs? Why are you thermally coupling all your subsystems separately? Why are you turning all CNT bonds into constraints? All these questions need to be answered before one starts taking trajectories seriously. Alex On 7/24/2018 5:49 AM, Atila Petrosian wrote: Dear Alex and gromacs users, I used trjconv -pbc whole. But my problem was not solved. You said "What I am trying to say is that per se nothing wrong seems to be happening". As I uderstood, in analyses such as gmx rms and gmx distanc and gmx traj (which I need them) this trajectory is not appropriate and should be corrected and modified. Which option of trjconv solve my pbc problem? Best regards, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] mpirun and gmx_mpi
On Tue, Jul 24, 2018 at 3:13 PM Mahmood Naderan wrote: > No idea? Those who use GPU, which command do they use? gmx or gmx_mpi? > > That choice depends on whether you want to run across multiple compute nodes; the former can not while the latter, as it is (by default) indicates that it's using an MPI library, can run across nodes. Both can be used on GPUs as long as the programs were built with GPU support. I recommend that you check the documentation: http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node -- Szilárd > Regards, > Mahmood > > > > > On Wednesday, July 11, 2018, 11:46:06 AM GMT+4:30, Mahmood Naderan < > nt_mahm...@yahoo.com> wrote: > > Hi,Although I have read the manual and I have wrote programs with mpi, > the gromacs use of mpi is confusing. > Is it mandatory to use mpirun before gmx_mpi or not? > Can someone shed a light on that? > > Regards, > Mahmood > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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] mpirun and gmx_mpi
No idea? Those who use GPU, which command do they use? gmx or gmx_mpi? Regards, Mahmood On Wednesday, July 11, 2018, 11:46:06 AM GMT+4:30, Mahmood Naderan wrote: Hi,Although I have read the manual and I have wrote programs with mpi, the gromacs use of mpi is confusing. Is it mandatory to use mpirun before gmx_mpi or not? Can someone shed a light on that? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] unusual trajectory
Dear Alex and gromacs users, I used trjconv -pbc whole. But my problem was not solved. You said "What I am trying to say is that per se nothing wrong seems to be happening". As I uderstood, in analyses such as gmx rms and gmx distanc and gmx traj (which I need them) this trajectory is not appropriate and should be corrected and modified. Which option of trjconv solve my pbc problem? Best regards, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] energy minimization
Dear Justin I used LigParGen server to generate ligand topology but I dont know what changes I have to do in .itp file. when I issued this command: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor faced this error:ERROR 1 [file LIG.itp, line 11]: Atomtype opls_800 not found I checked the aminoacids.rtp file of /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype opls_800 and 801 and ... in this file. while the LIG.itp which generated by LigParGen server has atomtype opls_800 , 801 and ... . I have to modify all of these atomtype opls_ in order to correspond to with aminoacid.rtp file? I would be thankfull if you help me. bestFraial On Monday, July 16, 2018, 5:29:17 PM GMT+4:30, Justin Lemkul wrote: On 7/16/18 3:49 AM, farial tavakoli wrote: > Dear Justin > > Thank you for your reply > I noticed my problem ( the reason was topolgen.pl name in my directory, it is > named topologen_1.1.pl in the working directory) > I generated my ligand topology but got this : > No output type specified. Using default type of .top > Unknown atom type: N 13 with 2 bonds - cannot assign atom type. > Using default H type for atom 16. > Using default H type for atom 26. > Using default H type for atom 31. > Using default H type for atom 38. > Using default H type for atom 39. > Using default H type for atom 40. > Using default H type for atom 41. > Unknown atom type: N 42 with 2 bonds - cannot assign atom type. > Using default H type for atom 47. > Using default H type for atom 48. > Using default H type for atom 49. > Using default H type for atom 50. > Using default H type for atom 51. > Using default H type for atom 52. > > > WARNING: Net charge on the molecule is -2.781 > You will need to make corrections to the output topology > > > TopolGen, version 1.1_dev (10/14/2009) complete. > > Output topology has been written. An attempt has been made to assign charges > and atom types based > on existing functional groups, but they may not be correct. No charge > calculations or other > parameterization calculations have been done. Guesses have been made for > charge groups. Please > inspect and correct the topology before using it in any simulations. The > author of the script does > NOT guarantee accuracy or usability of any of the content; TopolGen was > written as a convenience > for outputting a skeleton topology, and nothing more. Heed the above warning. TopolGen assigns parameters based on similarity to known functional groups. If your molecule has something unusual, it makes no attempt to try to assign reasonable parameters. You'll need to actually parametrize the molecule. Make use of available web servers like LikeParGen or others. -Justin > > the N13 atom connected to C with double bond. it sounds topolgen can not > identify N atom in 2 bonds with C . > would you please help me to figure out this problem > thans in advanceFarial > > On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul > wrote: > > > > On 7/15/18 1:38 AM, farial tavakoli wrote: >> Dear Justin >> >> But I copied & pasted topolgen and perl5 folders in the working directory. >> and faced the mentioned error. >> >> Can't open perl script "topolgen.pl": No such file or directory >> I dont know how I should figure out this problem. > The problem is still the same: there's nothing called "topolgen.pl" in > the working directory. List your files, you'll see it's called something > else. > >> Which one of all-atom force fields will you choose to run a simulation on a >> complex with small molecule, if you want to calculate binding energy using >> G_MMPBSA ?I really need your guidance . > Presumably any of them, but I don't do such calculations. > > -Justin > -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] question
Dear Mark and Alex, I want to use CNTs as drug carrier. I think I should consider water molecules inside the CNT. Do I think right? Best, AB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Energy decomposition
Dear all, I have followed the procedure you have suggested. Now I have a trajectory only containing my selected atoms and its related .tpr file. However, after running g_energy and selecting "total energy" I get an energy value which is too high in my opinion (i.e. 3.98246e+06 kj/mol). I feel something is going wrong. Have you got any idea? Furthermore, if I would decompose this total energy in bond term, stretch term, angle term etc etc, which would be the best way to do it? Thanks in advance for your contribute. V On Sun, Jul 8, 2018 at 8:17 PM, Vito GENNA wrote: > Dear Justin, > > Thanks a lot. > I indeed did not consider the idea to extrapolate only a part of the whole > trajectory. Nice shot. > Well, regarding the forcefield, this calculation in part is aiming to a > kind of “ff validation”. > > Thanks a lot for your prompt reply. > > V > > *Vito Genna, Ph.D* > PostDoctoral Researcher > Molecular Modelling and Bioinformatics > Orozco Lab > > *Dep. of Structural and Computational Biology* > *Institute for Research in Biomedicine (IRB Barcelona)* > Parc Científic de Barcelona > C/ Baldiri Reixac 10-12 > 08028 Barcelona > > P.S. This message has been written with my IPhone. Sorry for typo. > > Il giorno 08 lug 2018, alle ore 20:12, Justin Lemkul ha > scritto: > > > > On 7/8/18 2:06 PM, Vito GENNA wrote: > > Dear GMXusers, > > > I am writing you in the hope to find a solution to my problem. > > > I'd love (and truly love) calculate the intramolecular energy (both bonded > > and non-bonded terms) of a DNA backbone for which I have a .xtc trajectory > > (and of course coords). > > > What I did: > > > 1) defined the index.ndx for each DNA strand and generated a ndx.file > > cotaining [strand-1] and [System - (strand-1)] (works fine) > > > 2) Changed the energygrps in the mdp file to: [strand-1] [System - > > (strand-1)] (works fine) > > > 3) Generated a .tpr file selecting (from point 1) the .ndx of my interest > > > 4) with mdrun with -rerun option (by using the .tpr of my interest > > generated at the previous stage) I get the .edr file [strand-1] > > > 5) by using g_energy I only get Lennard-Jones and Coulomb terms (both short > > and long for [strand-1]:[strand-1]) while I would also include the > > bonded-terms. > > > 6) The option ETOT, provided by g_energy, I guess does not return the E of > > the strand, rather of the overall system. Isn't it? > > > Since I am comparing the same system in different conditions (then in > > different MD) I am looking for a strategy which would allow me to > > extrapolate all the energy terms for the backbone in a consistent fashion. > > > Did you ever calculated something similar? > > If so, how? > > > You need to extract only the coordinates you want from the trajectory with > trjconv and your index group. Then, create a matching .tpr file with only > those atoms using convert-tpr. Then use mdrun -rerun. Whether or not the > quantity means anything depends on how your force field was parametrized, > but that's how you calculate it. > > -Justin > > If not, any suggestion? > > > Thanks in advance for all your comments. > > > All the Best > > > VG > > > PS: Gromacs version: 5.0.4 > > > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- *** *Vito Genna, Ph.D* *Postoctoral Researcher* *Molecular Modeling and Bioinformatics* *Orozco Lab* *Institute for Research in Biomedicine (IRB Barcelona)* *Parc Centific de Barcelona* *C/ Baldiri Reixac 10-12* *08028 Barcelona* *** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)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] Parameters for manganese Mn2+
Dear all, perhaps a more general question: How do I convert Lennard Jones parameter from AMBER to GROMACS? Thank you! All the best Johanes On 23.07.2018 15:27, Hermann, Johannes wrote: Dear all, how can I convert AMBER parameters for usage in gromacs. In particular, I need parameters for manganese Mn2+. I found the corresponding AMBER parameters here: http://research.bmh.manchester.ac.uk/bryce/amber#ion Thank you very much! All the best Johannes -- __ *Technische Universität München* *Johannes Hermann, M.Sc.* Lehrstuhl für Bioverfahrenstechnik Boltzmannstr. 15 D-85748 Garching Tel: +49 8928915730 Fax: +49 8928915714 Email: j.herm...@lrz.tum.de http://www.biovt.mw.tum.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] question
Hi, What physical reality are you trying to model? Will it have water molecules inside the CNT? Mark On Mon, Jul 23, 2018, 16:19 Andrew Bostick wrote: > Hi, > > I want to do md simulation of adsorbsion on small molecule on cnt and > encapsulation small molecule into cnt. Should I remove water molecules > inside of cnt? > > Do these molecules interfere with the interaction between cnt and small > molecule? > > Thanks > AB > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)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.
