[gmx-users] DSSP output
Hi ALL, Is there any way to get the percentage of each secondary structural content of a protein using do_dssp if I supply a single PDB to it? And how to plot the data of the -sc output from do_dssp? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Projection of crystal structure on PCA plot
Thanks a lot Tsjerk :) -Anirban On Thu, Jun 6, 2013 at 4:42 PM, Tsjerk Wassenaar wrote: > Hi Anirban, > > Indeed. > > :) > > Tsjerk > > > On Thu, Jun 6, 2013 at 1:11 PM, Anirban >wrote: > > > Dear Tsjerk, > > > > Thank you very much for the explanation. > > > > So, in other words, as I have carried out PCA on the basis of CA atoms > from > > the MD trajectory, so if I wish to project the crystal structure onto the > > EV, then I need to consider only the CA atoms of the crystal structure > > (which in that case won't be the exact crystal structure) as well. Right? > > > > Thanks a lot again. > > > > Regards, > > > > Anirban > > > > On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar > > wrote: > > > > > Hi Anirban, > > > > > > The eigenvectors obtained from the simulation are a way of rewriting > the > > > coordinates of your structures, not in terms of atoms-XYZ, but as > > > combinations of these. Because they are combinations of atom-positions, > > > they are defined for the selection of atoms used for the calculation. > If > > > your crystal structure has the same atoms, which is true if you did not > > use > > > hydrogen atoms, or modeled parts for the covariance analysis, then you > > can > > > project that structure onto the eigenvectors determined, in exactly the > > way > > > you describe in your question. > > > > > > Hope it helps, > > > > > > Tsjerk > > > > > > > > > > > > On Thu, Jun 6, 2013 at 12:06 PM, Anirban < > reach.anirban.gh...@gmail.com > > > >wrote: > > > > > > > Hi ALL, > > > > > > > > I have carried out a simulation of a protein and have carried out PCA > > on > > > > the entire trajectory. I have obtained a 2D projection plot of EV1 on > > > EV2. > > > > Now I want to locate the conformation of the crystal structure (with > > > which > > > > I started the MD) on this map. How to do this? Can I use "g_anaeig -v > > > > Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n > > Prt_CA.ndx > > > > -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure > > > position? > > > > Or do I need to calculate covariance matrix for the crystal str.(I > > need a > > > > set of them in that case) and then use g_anaeig? > > > > Thanks a lot in advance. > > > > > > > > Regards, > > > > > > > > Anirban > > > > -- > > > > gmx-users mailing listgmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Projection of crystal structure on PCA plot
Dear Tsjerk, Thank you very much for the explanation. So, in other words, as I have carried out PCA on the basis of CA atoms from the MD trajectory, so if I wish to project the crystal structure onto the EV, then I need to consider only the CA atoms of the crystal structure (which in that case won't be the exact crystal structure) as well. Right? Thanks a lot again. Regards, Anirban On Thu, Jun 6, 2013 at 3:56 PM, Tsjerk Wassenaar wrote: > Hi Anirban, > > The eigenvectors obtained from the simulation are a way of rewriting the > coordinates of your structures, not in terms of atoms-XYZ, but as > combinations of these. Because they are combinations of atom-positions, > they are defined for the selection of atoms used for the calculation. If > your crystal structure has the same atoms, which is true if you did not use > hydrogen atoms, or modeled parts for the covariance analysis, then you can > project that structure onto the eigenvectors determined, in exactly the way > you describe in your question. > > Hope it helps, > > Tsjerk > > > > On Thu, Jun 6, 2013 at 12:06 PM, Anirban >wrote: > > > Hi ALL, > > > > I have carried out a simulation of a protein and have carried out PCA on > > the entire trajectory. I have obtained a 2D projection plot of EV1 on > EV2. > > Now I want to locate the conformation of the crystal structure (with > which > > I started the MD) on this map. How to do this? Can I use "g_anaeig -v > > Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx > > -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure > position? > > Or do I need to calculate covariance matrix for the crystal str.(I need a > > set of them in that case) and then use g_anaeig? > > Thanks a lot in advance. > > > > Regards, > > > > Anirban > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Projection of crystal structure on PCA plot
Hi ALL, I have carried out a simulation of a protein and have carried out PCA on the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2. Now I want to locate the conformation of the crystal structure (with which I started the MD) on this map. How to do this? Can I use "g_anaeig -v Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx -first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure position? Or do I need to calculate covariance matrix for the crystal str.(I need a set of them in that case) and then use g_anaeig? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat: joining randomized PDB files
Thanks a lot Justin, for the reply. But with -settime for every file I have to interactively give arbitrary values. I have around 500 PDB files for one part of the trajectory and there are total 10 parts. So its very difficult to repeat this for around 5000 times. Is there any other option. trjcat reads the randomized PDB files serially, so can't it just concatenate the files in that order? Or am I missing something? Thanks again. Regards, Anirban On Thu, May 9, 2013 at 7:07 PM, Justin Lemkul wrote: > > > On 5/9/13 9:35 AM, Anirban wrote: > >> Dear ALL, >> >> I want to randomize the frames of my trajectory for calculating >> convergence. For this, I have dropped the frames as PDB files using >> trjconv >> and then renamed them randomly. Now I want to join these randomized PDB >> frames to get a randomized trajectory using trajcat. But somehow trjcat >> always joins them in proper frame order (inspite of completely random PDB >> file names). How can I join the randomly to get a randomized trajectory? >> Any suggestion is welcome. >> >> > Use -settime and give them arbitrary time values. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjcat: joining randomized PDB files
Dear ALL, I want to randomize the frames of my trajectory for calculating convergence. For this, I have dropped the frames as PDB files using trjconv and then renamed them randomly. Now I want to join these randomized PDB frames to get a randomized trajectory using trajcat. But somehow trjcat always joins them in proper frame order (inspite of completely random PDB file names). How can I join the randomly to get a randomized trajectory? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Block average RMSD using g_analyze
Hi ALL, In order to see the convergence of a trajectory I am trying to calculate the RMSD error estimate using block averaging method which is implemented using g_analyze with -ee option. In it can I manually provide the block size or is it calculated based on the total simulation time? Another thing, is this method same as the block average RMSD method outlined by Alan Grossfield in JCTC 2011:7;2464-2472, in order to test convergence of a trajectory? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Lipid membrane partially broken and create huge voids after NVT
After NVT, usually the lipid bilayer move away from each other creating some voids, which occurs due to absence of pressure coupling. But its not a problem. You can go ahead and carry out NPT and see that bilayer has settled to normal position. -Anirban On Tue, Apr 9, 2013 at 3:04 PM, sdshine wrote: > Gromacs users, > > My complex heterogenous system has DPPC+ Protein+ligand. I have packed > lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2 > got > after 24th iteration) followed by adding solvent and neutralize the system > by adding CL35 & NA 39, since my system has -3.999 non zero total charge. > Then the minimized system has the energy -2.8989 with Max force= 9.58 > converged normally in step 464 step. > > I used lipid constraints in the file "DPOSRES_LIPID.itp" before NVT > > ; position restraint file for DPPC P8 > [ position_restraints ] > ; i funct fcxfcyfcz >81 0 0 1000 > --- > > My topology has the last part... > > --- > ; Include Position restraint file > #ifdef POSRES > #include "posre.itp" > #endif > > ; Include lig topology > #include "lig.itp" > > ; Strong position restraints for InflateGRO > #ifdef STRONG_POSRES > #include "DSTRONG_POSRES_B.itp" > #endif > > ; Include DPPC topology > #include "dppc.itp" > > ;strong position restraints for DPPC > #ifdef POSRES_LIPID > #include "DPOSRES_LIPID.itp" > #endif > > ; Include water topology > #include "spc.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > ; Include generic topology for ions > #include "ions.itp" > > [ system ] > ; Name > complex protein in water > > [ molecules ] > ; Compound#mols > Protein_G 1 > Lig 1 > DPPC 125 > SOL 3199 > CL 35 > NA 39 > --- > > There is no grompp error and no problem till NVT, after this > equillibration, > half of the DPPC along with SOL is no showing in VMD. Could any suggestions > on this behavior. > > Thanks in advance > > -Shine > > > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Lipid-membrane-partially-broken-and-create-huge-voids-after-NVT-tp5007128.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD with Xenon
On Mon, Apr 8, 2013 at 5:04 PM, Divya Sunil wrote: > hello, > > I have a protein in which I fixed Xenon in the binding sites. without > xenon, I used GROMOS96 53a6 force field for simulation. With Xenon, which > forcefield am I able to use? > Xenon is a non-standard molecule and you need to derive the parameters for it (refer to literature). Then you can use those parameters even with the 53a6 FF like any other non-standard molecule. > > thanking you > regards > > Divya > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] water molecule can not be settled
I thought the sole purpose of open source discussions and sharing is to help any scientific (or other) community to grow and benefit from each other, without taking into account the Nationality of the beneficiaries. If someone is willingly helping out somebody, whether Indian or not, in the GROMACS forum, then it should not bother Mr. Luis Felipe Pineda de Castro, since to the best of my knowledge it is not affecting him. I would request the moderators of this forum to take adequate measures about such postings as Mr. Castro's. Regards, Anirban On Fri, Apr 5, 2013 at 10:55 PM, Luis Felipe Pineda de Castro < luis.pinedadecas...@lnu.se> wrote: > After having followed for longer time the queries sent by some Indian > fellows, I wonder if it wouldn't more effective to arrange for a GROMACS > tutorial offered by Justin in an Indian location. Maybe you, the Indian > fellows, can arrange for the financing and invite Justin to hold such a > Tutorial on the basics of MD simulations and their implementation in > GROMACS. Considering the time Justin is spending responding to your > queries, maybe because you are devoid of adequate supervision or > theoretical background, this would be only fair. This posting is maybe a > little bit off topic, but somehow related. > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] > Sent: Friday, April 05, 2013 5:22 PM > To: Discussion list for GROMACS users > Subject: Re: Fw: [gmx-users] water molecule can not be settled > > You mean start over the NPT step? > > > > Sincerely, > Shima > > > - Original Message - > From: Justin Lemkul > To: Discussion list for GROMACS users > Cc: > Sent: Friday, April 5, 2013 7:50 PM > Subject: Re: Fw: [gmx-users] water molecule can not be settled > > On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh > wrote: > > > As I visualized the system, I see a water molecule somewhere between > lipid > > chains near the protein entrance. This has been happen during NPT. I' d > > like to delete this molecule but with such a kind of fatal error this > would > > impossible. So what's the way? Is there any tricky way to change > > coordinate of molecule? but I seems also impossible becasue PME problem! > > So whats the solution? > > > > > Delete the molecule, adjust your topology (and index file, if necessary), > and start over with the equilibration. > > -Justin > > -- > > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installation of GROMACS on server
On Tue, May 22, 2012 at 2:17 PM, Shima Arasteh wrote: > > Dear gmx users, > If I am not admin of the server, would it be possible that I install the > GROMACS 4.5.5 in my account (user) or upgrade the GROMACS version? > You can install latest version of GROMACS in your local directory by giving the "--prefix=YOUR_PATH" option with ./configure, without being the admin. -Anirban > Thanks for your suggestions in advance. > Sincerely, > Shima > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] intermolecular H bond selection
On Mon, May 21, 2012 at 3:09 AM, mu xiaojia wrote: > Thanks for prompt answering but I may need to clarify my question and > sorry for the understanding, > > For example, I have dipeptides like Ala-Ala, how to ask g_hbond only > calculate the h bonds between Ala on different dipeptides instead of > counting all the possible h bonds between Ala(intermolecularly and > intramolecularly) > > Make two groups with make_ndx that contains the residue numbers (or specific atom numbers) of the ALA residues between which you want to count the H bonds and then select these group numbers with g_hbond. -Anirban > Thanks very much! > > > On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul wrote: > >> >> >> On 5/18/12 7:22 PM, mu xiaojia wrote: >> >>> Hi gmx-users, >>> >>> I have a question might be explained before but I cannot understand from >>> the >>> previous , how to calculation the intermolecular h-bonds between two >>> molecules? >>> I saw someone mentioned using a second tpr file, but how to do it >>> specifically? >>> Thanks very much! >>> >>> >> g_hbond asks for two index groups to be selected. Assign each molecule >> to an index group and select them when prompted. >> >> -Justin >> >> -- >> ==**== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> ==**== >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] extention of the simulation
On Sat, May 19, 2012 at 3:21 PM, Turgay Cakmak wrote: > > Hi Gromacs users, > > > I have a question related to the extension of the simulation. > > I have done 10 ns simulation (several peptides in a box). Now, I want to > extend it 10ns more. > > > >- As far as I see from “Justin Lemkul’s Lysozyme in water tutorial”, >to extend simulation, following should be done. > > grompp -f grompp.mdp -c first10ns.gro –t first10ns.cpt -p > topol.top -o second10ns.tpr > > > >- But, another tutorial says that: > > tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr > –until $VALUE > > Where $VALUE = ps (e.g. if you wanted to extend a 2 ns run to > 5 ns, then $VALUE = 5000) > > This option is fine. You don't need the .trr and .edr files if you supply a check-point file (.cpt) with -f option, to extend a simulation. -Anirban > > I am confused which one shuld have used. So, if someone could help me, I > would be happy. > > Turgay > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding error.
On Fri, May 18, 2012 at 12:20 PM, Seera Suryanarayana wrote: > Dear all, > While i am running gromacs software i am getting following > error.Let me know that error how to over come. > > > Fatal error: > Residue 'CSD' not found in residue topology database First read: http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Anirban > > > > > Suryanarayana Seera, > PhD student, > Hyderabad, > India. > > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Software inconsistency error with GROMACS4.5.5
Hi ALL, I am running a protein+lipid+water+ions simulation using GROAMCS4.5.5 (compiled with intel compilers on RedHat OS). The EM, NVT and few thousand steps of NPT ran fine beforw throwing up the following error: --- Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Bond of 36787 missing 2 U-B of 70200 missing 3 Proper Dih. of 124764 missing 6 LJ-14 of 98070 missing 12 exclusions of 277654 missing 9 --- Program mdrun_mpi, VERSION 4.5.5 Source code file: domdec_top.c, line: 173 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Why is this error coming? Is it a bug? Any suggestion is welcome. Thanks and regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parameterization of new metal ion
On Thu, May 17, 2012 at 11:47 AM, priya thiyagarajan < priya.thiyagaraja...@gmail.com> wrote: > Respected sir, > > i want to add metal ions Ni2+ and co2+ during my simulation. > > can anyone help me how to set parameters to define new ion Ni2+ and co2+ > in gromacs forcefield.. > > i edited in ions.itp file and tried but i got error atomtype not found.. > You need to modify the .rtp file as well. Follow this: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Anirban > > can anyone please explain me elaborately how to set parameters .. > > please help me with your answer.. > > Thanking you, > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Coupling groups in protein-ligand-lipid simulation
Hi ALL, I am simulating a membrane protein docked with a ligand and embedded in a lipid bilayer. For COM removal I am using two groups, "Prt_Lig_Lipid" and "SOL_CL". For temperature and pressure couplings should I use these two groups or should I use three groups, "Protein", "Lipid" and "Lig_SOL_CL"? Any suggestion is welcome. Thanks and regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ATB & SWISSPARAM Topologies
Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to carry out manual checks like that required for PRODRG outputs? Any suggestion is welcome. Thanks and regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about the frame selection
On Tue, May 15, 2012 at 11:48 AM, rama david wrote: > > Thank you ANIRBAN for your reply .. > > >> I think its better to remove the periodicity when you are going to start >> a fresh simulation with this protein. >> Could you told me how to remove the periodicity ??? >> > You can use trjconv with "-pbc mol -ur compact" options. But first look into trjconv -h -Anirban > > >> >>> Thank you in advance ... >> >> > >> >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about the frame selection
On Tue, May 15, 2012 at 11:26 AM, rama david wrote: > Hi Gromacs Users , >I simulated a 4 peptide in a box . > After completion of 30 ns simulattion , I extract > the particular time frame 29000 ps of my interest. > Now I want these frame for my next simulations > study .. > In one simulation I want to keep the box size same as the > mentioned in extracted pdb and in another one I need to change the size > of box to > 70 70 70 > > > REMARKGENERATED BY TRJCONV > TITLE Protein in water t= 29000.0 > REMARKTHIS IS A SIMULATION BOX > CRYST1 45.096 45.096 45.096 90.00 90.00 90.00 P 1 1 > MODEL1 > > So my queries are like > > 1. Should I used the extracted frame directly for further study or > I need to remove the periodicity...?? > I think its better to remove the periodicity when you are going to start a fresh simulation with this protein. > > 2 . to change the box size how to proceed ?? > Should I delete the line manually and adjust the box size > You can change the box dimensions with editconf using the -box (desired dimensions) option. -Anirban > > > All suggestion are welcome ... > > > Than you in advance > > rama david > > > > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ATB & SWISSPARAM Topologies
Thanks a lot Justin! On Tue, May 15, 2012 at 4:20 PM, Justin A. Lemkul wrote: > > > On 5/15/12 5:54 AM, Anirban wrote: > >> Hi ALL, >> >> How accurate are the topologies of non-standard molecules generated by >> ATB or >> SWISSPARAM for GROMACS? Are they acceptable for publications? Are we >> required to >> carry out manual checks like that required for PRODRG outputs? >> Any suggestion is welcome. >> >> > I would always verify parameters before running real production > simulations. I believe ATB and SwissParam are, in general, far more > reliable than PRODRG, but I doubt it can be stated universally that any > automated method is inherently flawless. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun_mpi issue with CHARMM36 FF
On Mon, May 14, 2012 at 11:35 AM, Mark Abraham wrote: > On 14/05/2012 3:52 PM, Anirban wrote: > > Hi ALL, > > I am trying to simulate a membrane protein system using CHARMM36 FF on > GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of > arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using > mpirun and gives proper output. But whenever I try to submit it on more > than 5 nodes, the job gets killed with the following error: > > > That's likely going to be an issue with the configuration of your MPI > system, or your hardware, or both. Do check your .log file for evidence of > unsuitable DD partiion, though the fact of "turning on dynamic load > balancing" suggest DD partitioning worked OK. > > Mark > > Hello Mark, Thanks for the reply. The .log file reports no error/warning and ends abruptly with the following last lines: Making 3D domain decomposition grid 4 x 3 x 9, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: Protein_POPC 1: SOL_CL There are: 117548 Atoms Charge group distribution at step 0: 358 353 443 966 1106 746 374 351 352 352 358 454 975 1080 882 381 356 357 357 358 375 770 1101 882 365 359 358 351 348 487 983 1051 912 377 344 361 363 352 596 1051 1036 1050 553 351 349 366 352 375 912 1125 1045 478 351 344 356 362 445 971 1040 959 520 405 355 357 355 639 1032 1072 1096 790 474 353 349 345 449 1019 1047 971 444 354 357 355 357 391 946 1093 904 375 367 368 349 349 409 934 1082 867 406 350 350 364 341 398 978 1104 937 415 341 368 Grid: 6 x 7 x 4 cells Initial temperature: 300.318 K Started mdrun on node 0 Fri May 11 20:43:52 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) U-BProper Dih. Improper Dih. CMAP Dih. LJ-14 8.67972e+046.15820e+041.38445e+03 -1.60452e+031.44395e+04 Coulomb-14LJ (SR) Coulomb (SR) Coul. recip. Potential -5.21377e+044.98413e+04 -1.21372e+06 -8.94296e+04 -1.14284e+06 Kinetic En. Total EnergyTemperature Pressure (bar) Constr. rmsd 2.93549e+05 -8.49294e+053.00132e+02 -1.80180e+011.40708e-05 ------- Any suggestion is welcome. Thanks, Anirban > > > > - > > starting mdrun 'Protein' > 5000 steps, 10.0 ps. > > NOTE: Turning on dynamic load balancing > > Fatal error in MPI_Sendrecv: Other MPI error > Fatal error in MPI_Sendrecv: Other MPI error > Fatal error in MPI_Sendrecv: Other MPI error > > > = > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 256 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > = > [proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb > (./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed > [proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event > (./tools/demux/demux_poll.c:77): callback returned error status > [proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error > waiting for event > . > . > . > > ------ > > Why is this happening? Is it related to DD and PME? How to solve it? Any > suggestion is welcome. > Sorry for re-posting. > > > Thanks and regards, > > Anirban > > > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@grom
[gmx-users] mdrun_mpi issue with CHARMM36 FF
Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on more than 5 nodes, the job gets killed with the following error: - starting mdrun 'Protein' 5000 steps, 10.0 ps. NOTE: Turning on dynamic load balancing Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error = = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 256 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES = [proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed [proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status [proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error waiting for event . . . -- Why is this happening? Is it related to DD and PME? How to solve it? Any suggestion is welcome. Sorry for re-posting. Thanks and regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdrun_mpi issue for CHARMM36 FF
Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on more than 5 nodes, the job gets killed with the following error: - starting mdrun 'Protein' 5000 steps, 10.0 ps. NOTE: Turning on dynamic load balancing Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error = = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 256 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES = [proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed [proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status [proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error waiting for event . . . -- Why is this happening? Is it related to DD and PME? How to solve it? Any suggestion is welcome. Sorry for re-posting. Thanks and regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of POPC in water using CHARMM27
On Sat, May 12, 2012 at 9:49 AM, Shima Arasteh wrote: > Dear gmx users, > > Anybody can guide me to some articles which introduces CHARMM36 > forcefield? I want to study about this forcefield. > > Have a look at this paper: http://pubs.acs.org/doi/abs/10.1021/jp101759q -Anirban Thanks in advance, > Shima > > ------ > *From:* Anirban > *To:* Shima Arasteh ; Discussion list for > GROMACS users > *Sent:* Friday, May 11, 2012 9:22 PM > > *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27 > > > > On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > > CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a > good output of simulation. > Before this, Justin also suggested me for CHARMM36. Ok, I will use > CHARMM36. But about the atom types, it's not still clear for me what I need > to do. If I use the CHARMM36, am I supposed to build berger lipids? > > > Actually if you use CHARMM36 FF then no need to use Berger parameters, > since CHARMM36 FF already have the all-atom POPC parameters. But there are > differences among the atom types. So you can use these POPC files (Peter > Lai provided me these files and these were generated for the following > work: (please reference): > Lai, P.C. and Crasto, C.J. > Beyond Modeling: All-Atom Olfactory Receptor Model Simulations > Front. Gene. > Volume 3 Year 2012 Number 61 > DOI: 10.3389/fgene.2012.00061) > > These files worked fine for me (with grompp). Include the popc.itp file in > your .top file. > > -Anirban > > > Thanks, > Shima > > -- > *From:* Anirban > *To:* Shima Arasteh > *Sent:* Friday, May 11, 2012 8:58 PM > > *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27 > > > > On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > > Dear Anirban, > No, I have not done. Because I didn't know I need Berger lipids for this > simulation. > > > Actually I think the coordinate and topology files from Tieleman's site > are in accordance with the Berger lipid parameters and hence works with the > united-atom gromos FF. You can also get CHARMM27 lipids from > http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the > atom-type errors can be solved if you can build a proper .hdb file with the > proper corrections for the violating atom names. > > -Anirban > > > Thanks for you reply, > Cheers, > Shima > >-- > *From:* Anirban > *To:* Shima Arasteh ; Discussion list for > GROMACS users > *Sent:* Friday, May 11, 2012 8:10 PM > *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27 > > > > On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > > Dear gmx users, > > I'm going to simulate the POPC in water. > I downloaded required files in Tielman site and made the .top file. Then > included the CHARMM27.ff in the .top file. > When I run the grompp I get the fatal error as below: > Atomtype CB not found > > I have done the same with gromos87.ff . But I didn't see any error. > What's the problem? > Anybody may suggest me how to solve this problem? Is this because of the > forcefield? Or something in .top file goes wrong? > > > Have properly edited the CHARMM27 bonded and nonbonded .itp files to > include the Berger lipid parameters and have you included the POPC > topology? You can follow this tutorial to get an idea: > > https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial > > -Anirban > > > Thanks, > Shima > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of POPC in water using CHARMM27
On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh wrote: > CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a > good output of simulation. > Before this, Justin also suggested me for CHARMM36. Ok, I will use > CHARMM36. But about the atom types, it's not still clear for me what I need > to do. If I use the CHARMM36, am I supposed to build berger lipids? > > Actually if you use CHARMM36 FF then no need to use Berger parameters, since CHARMM36 FF already have the all-atom POPC parameters. But there are differences among the atom types. So you can use these POPC files (Peter Lai provided me these files and these were generated for the following work: (please reference): Lai, P.C. and Crasto, C.J. Beyond Modeling: All-Atom Olfactory Receptor Model Simulations Front. Gene. Volume 3 Year 2012 Number 61 DOI: 10.3389/fgene.2012.00061) These files worked fine for me (with grompp). Include the popc.itp file in your .top file. -Anirban > Thanks, > Shima > > -- > *From:* Anirban > *To:* Shima Arasteh > *Sent:* Friday, May 11, 2012 8:58 PM > > *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27 > > > > On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > > Dear Anirban, > No, I have not done. Because I didn't know I need Berger lipids for this > simulation. > > > Actually I think the coordinate and topology files from Tieleman's site > are in accordance with the Berger lipid parameters and hence works with the > united-atom gromos FF. You can also get CHARMM27 lipids from > http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the > atom-type errors can be solved if you can build a proper .hdb file with the > proper corrections for the violating atom names. > > -Anirban > > > Thanks for you reply, > Cheers, > Shima > >-- > *From:* Anirban > *To:* Shima Arasteh ; Discussion list for > GROMACS users > *Sent:* Friday, May 11, 2012 8:10 PM > *Subject:* Re: [gmx-users] Simulation of POPC in water using CHARMM27 > > > > On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > > Dear gmx users, > > I'm going to simulate the POPC in water. > I downloaded required files in Tielman site and made the .top file. Then > included the CHARMM27.ff in the .top file. > When I run the grompp I get the fatal error as below: > Atomtype CB not found > > I have done the same with gromos87.ff . But I didn't see any error. > What's the problem? > Anybody may suggest me how to solve this problem? Is this because of the > forcefield? Or something in .top file goes wrong? > > > Have properly edited the CHARMM27 bonded and nonbonded .itp files to > include the Berger lipid parameters and have you included the POPC > topology? You can follow this tutorial to get an idea: > > https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial > > -Anirban > > > Thanks, > Shima > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of POPC in water using CHARMM27
On Fri, May 11, 2012 at 9:10 PM, Anirban wrote: > > > On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh < > shima_arasteh2...@yahoo.com> wrote: > >> Dear gmx users, >> >> I'm going to simulate the POPC in water. >> I downloaded required files in Tielman site and made the .top file. Then >> included the CHARMM27.ff in the .top file. >> > Its better to use CHARMM36 FF. It is more accurate towards the lipids and available from the GROMACS user contribution section. > When I run the grompp I get the fatal error as below: >> Atomtype CB not found >> >> I have done the same with gromos87.ff . But I didn't see any error. >> What's the problem? >> Anybody may suggest me how to solve this problem? Is this because of the >> forcefield? Or something in .top file goes wrong? >> >> > Have properly edited the CHARMM27 bonded and nonbonded .itp files to > include the Berger lipid parameters and have you included the POPC > topology? You can follow this tutorial to get an idea: > > https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial > > -Anirban > > >> Thanks, >> Shima >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of POPC in water using CHARMM27
On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh wrote: > Dear gmx users, > > I'm going to simulate the POPC in water. > I downloaded required files in Tielman site and made the .top file. Then > included the CHARMM27.ff in the .top file. > When I run the grompp I get the fatal error as below: > Atomtype CB not found > > I have done the same with gromos87.ff . But I didn't see any error. > What's the problem? > Anybody may suggest me how to solve this problem? Is this because of the > forcefield? Or something in .top file goes wrong? > > Have properly edited the CHARMM27 bonded and nonbonded .itp files to include the Berger lipid parameters and have you included the POPC topology? You can follow this tutorial to get an idea: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial -Anirban > Thanks, > Shima > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MPIRUN issue for CHARMM36 FF
Hi ALL, I am trying to simulate a membrane protein system using CHARMM36 FF on GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using mpirun and gives proper output. But whenever I try to submit it on more than 5 nodes, the job gets killed with the following error: - starting mdrun 'Protein' 5000 steps, 10.0 ps. NOTE: Turning on dynamic load balancing Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error Fatal error in MPI_Sendrecv: Other MPI error = = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 256 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES = [proxy:0:0@cn034] HYD_pmcd_pmip_control_cmd_cb (./pm/pmiserv/pmip_cb.c:906): assert (!closed) failed [proxy:0:0@cn034] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status [proxy:0:0@cn034] main (./pm/pmiserv/pmip.c:214): demux engine error waiting for event . . . -- Why is this happening? Is it related to DD and PME? How to solve it? Any suggestion is welcome. Thanks and regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Justin lipid-position restraine
On Tue, May 8, 2012 at 1:01 PM, rama david wrote: > > > On Tue, May 8, 2012 at 1:00 PM, rama david wrote: > >> Hi Gromacs user, >> I am doing the justin tutorial on lipid posted on link.. >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html >> >> I am following the tutorial very carefully ... >> As mentioned in the tutorial I need to generate strong position >> restrained on >> proteins heavy atoms to ensure that position of atom does not change >> during EM >> (Energy Minimisation ) >> My command line is as follow . >> >> genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 10 10 10 >> >> >> >> Reading structure file >> Select group to position restrain >> Group 0 ( System) has 138 elements >> Group 1 (Protein) has 138 elements >> Group 2 ( Protein-H) has 109 elements >> Group 3 (C-alpha) has16 elements >> Group 4 ( Backbone) has48 elements >> Group 5 ( MainChain) has64 elements >> Group 6 ( MainChain+Cb) has78 elements >> Group 7 (MainChain+H) has81 elements >> Group 8 ( SideChain) has57 elements >> Group 9 (SideChain-H) has45 elements >> Select a group: >> >> >> >> I am using Gromacs 4.5.4 >> >> Generally position restrain is applied on backbone of protein >> So I choose backbone (4) >> >> Is it right or I have to choose the group protein(138 elements) to apply >> position restraine on all protein atoms >> >> As the tutorial suggest you can restrain the heavy atoms, but I usually restrain the entire protein during the InflateGro steps (EMs) and let the lipids minimize around it. -Anirban > >> >>All suggestions are welcome >>thank you in advance >> >> >> Rama David . >> >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] itp file problem
On Mon, May 7, 2012 at 5:11 PM, Sarath Kumar Baskaran < bskumar.t...@gmail.com> wrote: > > First i had simulation of the protein alone in united atom gromacs force > field by -ff gmx in pdb2gmx > now i am unable to run the protein-ligand complex for the same protein > with a ligand, > it says the following error due to itp file generated from PRODRG, > if i change the force field its says atom mismatch. Please > help me > Change the force-field means? Did you change the FF with pdb2gmx, or just in your .top file? > > What is the way to run the simulation > > grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr > :-) G R O M A C S (-: > >GRoups of Organic Molecules in ACtion for Science > > :-) VERSION 4.0.7 (-: > > > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. >Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2008, The GROMACS development team, > check out http://www.gromacs.org for more information. > > This program is free software; you can redistribute it and/or > modify it under the terms of the GNU General Public License > as published by the Free Software Foundation; either version 2 > of the License, or (at your option) any later version. > > :-) grompp-4.0.7 (-: > > Option Filename Type Description > > -f em.mdp Input, Opt! grompp input file with MD parameters > -po mdout.mdp Output grompp input file with MD parameters > -c prt_b4ion.pdb InputStructure file: gro g96 pdb tpr tpb tpa > -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa > -n index.ndx Input, Opt. Index file > -pprt.top InputTopology file > -pp processed.top Output, Opt. Topology file > -o prt_b4ion.tpr Output Run input file: tpr tpb tpa > -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt > -e ener.edr Input, Opt. Energy file: edr ene > > Option Type Value Description > -- > -[no]h bool no Print help info and quit > -niceint0 Set the nicelevel > -[no]v bool yes Be loud and noisy > -timereal -1 Take frame at or first after this time. > -[no]rmvsbds bool yes Remove constant bonded interactions with > virtual > sites > -maxwarn int0 Number of allowed warnings during input > processing > -[no]zerobool no Set parameters for bonded interactions without > defaults to zero instead of generating an error > -[no]renum bool yes Renumber atomtypes and minimize number of > atomtypes > > Ignoring obsolete mdp entry 'title' > Ignoring obsolete mdp entry 'cpp' > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# > checking input for internal consistency... > processing topology... > Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmx.itp > Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxnb.itp > Opening library file /usr/local/gromacs-4.0.7//share/top/ffgmxbon.itp > Opening library file /usr/local/gromacs-4.0.7//share/top/ff_dum.itp > Generated 1284 of the 1485 non-bonded parameter combinations > Opening library file /usr/local/gromacs-4.0.7//share/top/spc.itp > Opening library file /usr/local/gromacs-4.0.7//share/top/ions.itp > > --- > Program grompp-4.0.7, VERSION 4.0.7 > Source code file: toppush.c, line: 947 > > Fatal error: > Atomtype CR1 not found > --- > > "I Caught It In the Face" (P.J. Harvey) > > Did you include the ligand's itp file in your .top file? I think you haven't. > [ > > grompp-4.0.7 -f em.mdp -c prt_b4ion.pdb -p prt.top -o prt_b4ion.tpr > :-) G R O M A C S (-: > > GROtesk MACabre and Sinister > > :-) VERSION 4.0.7 (-: > > > Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. >Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2008, The GROMACS development team, > check out http://www.gromacs.org for more information. > > This program is free software; you can redistribute it and/or > modify it under the terms of the GNU General Public License > as published by the Free Software Foundation; either version 2 > of the License, or (at your option) any later version. > >
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Mon, May 7, 2012 at 10:17 AM, Bala S wrote: > Justin and Anirban, > > I have another query on membrane simulation following your tutorials. > > How do I insert only a part of protein into the lipid bilayer and carryout > the simulation? > editconf with -box option helps you to orient your protein with respect to the bilayer. And visually in VMD you have the option of move a "molecule" under "mouse" option in which you can move your protein wrt the bilayer (when the bilayer and the protein .gro/.pdb files are loaded separately in VMD). -Anirban > > Thanks > Bala S > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4957017.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CHARMM36 and Dispersion correction
Hi ALL, I am simulating a membrane protein immersed in a POPC bilayer using CHARMM36 FF in GROMACS 4.5.5. In NVT and NPT (i.e. in equilibration and production runs) should I use the dispersion correction or not (as suggested in some previous posts)? And if NOT using dispersion correction, then should I use "vdwtype" as "switch"? Any suggestion is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] jointly-couple lipids to theromstat - MARTINI force-field
On Thu, May 3, 2012 at 5:17 PM, Weingarth, M.H. wrote: > Hello, > > I am a bit confused by a comment which I find in all MARTINI example > md.mdp scripts concerning the tc-groups : > > It is stated there to couple groups separately: > > << MARTINI -Normal temperature and pressure coupling schemes can be used. > It > ; is recommended to couple individual groups in your system seperately>> > > I am simulating a mixed dppc:dppg membrane (see below my parameters). Even > these two different lipids-types should be coupled separately? (and how > about Na+ (Qd particles) and water - also separately?) > > I would greatly appreciate any comment on this issue. > > Thanks a lot > Markus > > > > my parameter: > ; Temperature coupling: > tcoupl = berendsen > ; Groups to couple separately: > tc-grps = DPPC DPPG W NAA Protein > > Generally in membrane protein simulations different coupling groups are used to increase the accuracy of the calculations (more realistic). In your system you can make make three groups: Protein, Lipids(DPPC+DPPG) and Sol+Ions(Na+Qd) -Anirban > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] membrane simulation
On Thu, May 3, 2012 at 4:38 PM, wrote: > Hi all, > I'm new in Membrane simulations with Gromacs. I have to simulate a system > made up of a protein just leant on a membrane patch which has previously > been extended and made it free of periodicity (with trjconv). I'm reading > the "KALP15 in DPPCI" Tutorial and, so far, I managed to obtain my protein > (in pdb code) very close to the membrane surface by using editconf and cat > command. At this point, I don't know how to get on. 1)How should I > generate the topology file which includes the coordinates both of the > protein and of the membrane? > If you are using the ff53a6 FF then you need to add the appropriate lipid parameters in the ffnonbonded.itp and ffbonded.itp files (of ff53a6 FF) files which is very well explained in the tutorial. Then in your .top file you need to include the DPPC.itp. However, if you are using CHARMM36 FF, then you can directly use pdb2gmx on your system (I suppose DPPC is already included in it). If you wish to use the ff43a1 FF, then you can find the modified .itp files at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial . > 2)Furthermore, the lipid molecules are listed in my pdb file with the > abbreviation "DPP", whereas I see that those ones are called "DPPC" in the > Tutorial. Therefore, Should I replace "DPP" abbreviation with "DPPC" in my > pdb file? Could this difference cause any bugs in the next steps? > PDB files use three letter convention for residue names. I think you can change them without any issue in the .gro file. -Anirban > Any suggestion would be appreciated, > > Silvia > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 format POPC
Thanks a lot Peter. Will try out with this. -Anirban On Wed, May 2, 2012 at 9:42 PM, Peter C. Lai wrote: > http://uab.hyperfine.info/~pcl/files/popc36/ > > These were generated for the following work: (please reference): > Lai, P.C. and Crasto, C.J. > Beyond Modeling: All-Atom Olfactory Receptor Model Simulations > Front. Gene. > Volume 3 Year 2012 Number 61 > DOI: 10.3389/fgene.2012.00061 > > On 2012-05-02 05:49:17PM +0530, Anirban Ghosh wrote: > > Hi ALL, > > > > I was looking for a CHARMM36 format (atom-types) equilibrated POPC > bilayer > > (PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one > > from Dr. Klauda's site ( > > http://terpconnect.umd.edu/~jbklauda/research/download.html), but that > > popc.pdb (under CHARMM36 FF) seem to have different atom-types (like P1 > in > > place of P, etc.) and hence pdb2gmx throws up error when processed with > > CHARMM36 FF option. Is there any CHARMM36 FF format equilibrated POPC > > bilayer available online, or can someone provide, please? > > Thanks a lot in advance. > > > > > > Regards, > > > > Anirban > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > == > Peter C. Lai| University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > == > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CHARMM36 format POPC
Hi ALL, I was looking for a CHARMM36 format (atom-types) equilibrated POPC bilayer (PDB/GRO) to use with the CHARMM36 FF in GROAMCS 4.5.5. I downloaded one from Dr. Klauda's site ( http://terpconnect.umd.edu/~jbklauda/research/download.html), but that popc.pdb (under CHARMM36 FF) seem to have different atom-types (like P1 in place of P, etc.) and hence pdb2gmx throws up error when processed with CHARMM36 FF option. Is there any CHARMM36 FF format equilibrated POPC bilayer available online, or can someone provide, please? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats
Thanks Angel and Justin. Will try out the options! Regards, -Anirban On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul wrote: > > > On 5/1/12 8:05 AM, Ángel Piñeiro wrote: > >> I guess there are better solutions but an alternative is to map your >> bilayer to >> MARTINI >> (http://md.chem.rug.nl/**cgmartini/<http://md.chem.rug.nl/cgmartini/>) >> and then to use SUGAR-PIE >> (http://smmb.usc.es/sugarpie/**sugarpie.php<http://smmb.usc.es/sugarpie/sugarpie.php>) >> to go to from MARTINI to all-atom >> CHARMM36. >> >> > Even simpler would be to fix the offending atom names and build a suitable > .hdb entry (if one does not already exist) and produce the topology with > pdb2gmx. I would think it would then be far easier to preserve the > original configurations of the lipids, rather than changing the resolution > back and forth. > > -Justin > > Hope it helps, >> >> Ángel. >> >> >> On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote: >> >>> Hi ALL, >>> >>> >>> I have a equilibrated POPC bilayer (100 ns run) that I have run using >>> GROMOS >>> ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation >>> using >>> CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming >>> conventions >>> (N, P, C, O) between this two FFs as a result of which pdb2gmx gives >>> error. >>> Can these atom names (hydrogens can be ignored) of my equilibrated POPC >>> bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot >>> in >>> advance. >>> >>> >>> >>> >>> Regards, >>> >>> >>> Anirban >>> -- >>> gmx-users mailing listgmx-us...@gromacs.org >> gmx-users@gromacs.org> >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> Please search the archive athttp://www.gromacs.org/** >>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search> >>> before posting! >>> >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it >>> togmx-users-request@gromacs.**org >> gmx-users-request@**gromacs.org >. >>> Can't post? >>> Readhttp://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> >> >> >> > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] POPC: ff53a6 and CHARMM36 formats
Hi ALL, I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions (N, P, C, O) between this two FFs as a result of which pdb2gmx gives error. Can these atom names (hydrogens can be ignored) of my equilibrated POPC bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding error
On Mon, Apr 30, 2012 at 11:50 AM, seera suryanarayana wrote: > Respected Sir, > > While i am running the gromacs software to simulate > the protein i am getting the following error. > > Fatal error: > Residue 'GNP' not found in residue topology database > > http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Anirban > > Suryanarayna Seera, > PhD student. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Question about starting Gromacs 4.5.4 parallel runs using mpirun
On Sat, Apr 28, 2012 at 10:22 PM, Andrew DeYoung wrote: > Hi, > > Typically, I use Gromacs 4.5.5 compiled with automatic threading. As you > know, automatic threading is awesome because it allows me to start parallel > runs without calling mpirun. So on version 4.5.5, I can start a job on > eight > CPUs using simply the command: > > mdrun -s topol.tpr -nt 8 > > However, now I am using a different node on my department's cluster, and > this node instead has Gromacs 4.5.4 (compiled without automatic threading). > So, I must use mpirun to start parallel runs. I have tried this command: > > mpirun -machinefile mymachines -np 8 mdrun -s topol.tpr > > I suppose this mdrun executable is not mpi-enabled. Have you compiled mdrun with "--enable-mpi" option? -Anirban > where mymachines is an (extensionless) file containing only the text "c60 > slots=8". (c60 is the name of the node that I am using.) > > I get this error message: > > "Missing: program name. Program mdrun either does not exist, is not > executable, or is an erroneous argument to mpirun." > > This is strange, because mdrun is, I think, in my path. For example, if I > type "mdrun -h", I get the manual page for mdrun (version 4.5.4). > > Then I tried the command "which mdrun", and it gave me this output: > > /usr/local/gromacs/bin/mdrun > > So, next I tried to call mdrun via mpirun using the specific path for > mdrun: > > mpirun -machinefile mymachines -np 8 /usr/local/gromacs/bin/mdrun -s > topol.tpr > > This starts running my simulation, but when I look in "top", the simulation > is only running on a single CPU; there is only one entry for mdrun in > "top", > and it has only %CPU=100 (not eight different entries for mdrun, nor one > entry with %CPU=800). Also, the simulation is going at the speed I would > expect for running on a single CPU -- it is very slow, so I am convinced > that, as "top" suggests, mdrun is running on only one CPU. > > Strangely, my colleagues are able to run jobs in parallel using the exact > commands that I described above. So apparently something is wrong with my > user ID, although there are no error messages (except the error message > about "Missing: program name" that I described). > > If you have time, do you have any suggestions for other things that I can > try? Do you think that something could be wrong with my bashrc file? > > Thanks for your time! > > Andrew DeYoung > Carnegie Mellon University > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul wrote: > > > On 4/27/12 10:00 AM, Bala S wrote: > >> Anirban, >> >> Exactly.. That's the gap (either side of the leaflets) I was mentioning >> about. I'll try EM and check itagain. >> >> > EM won't fill in solvent gaps. If you're using my protocol for increasing > the C radius in vdwradii.dat, then a small gap is normal and will close > when doing equilibration as the solvent fills in around the lipid > headgroups. > > Yes, as Justin mentioned, the equilibration runs (restraining the protein) will fill those gaps. Anirban -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 7:00 PM, Bala S wrote: > Anirban, > > Thank you. You guys are doing miracles with the biomolecules and solving > almost all of my problems. > > I have followed your suggestion and could see now some more SOL molecules > by > increasing the z value. > > But I am seeing a substantial gap between the surface of the lipid bilayer > and added SOL molecules in the visualizer. Is it normal or I have to do > something about it? > > I didn't really get your point. From the surface means on either side of the leaflets? Or one thing you can do is to carry out the EM, and equilibration runs (NVT and NPT) (restraining the protein) and see how the waters orient them with respect to the bilayer. Anirban > Thanks > Bala S > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933923.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 6:31 PM, Bala S wrote: > Justin, > > OOPS!! > Sorry for that.. Now I could realize it. > Following up.. I have done further iterations with inflategro and reached > 0.62 nm^2 which similar to what you have explained in the tutorial. > > Now, I could see the lipid bilayer really shrinked and no SOL molecules are > seen in between. Now the issue I would like to have clarification on is > that > only 163 SOL molecules were added up and down which looks very scarce for > the simulation. > > What is the solution? > > First visualize and see whether the hydrophilic ends of the lipid bilayer and your protein's part on either side of the bilayer (like a GPCR's intra and extra cellular ends) are well immersed in the water box. If not, you can increase the solvation box along the z-axis by increasing the z value for -box option in editconf (keeping x and y values same). Anirban > Bala S > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933854.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 4:59 PM, Justin A. Lemkul wrote: > > > On 4/27/12 6:40 AM, Bala S wrote: > >> Thanks for the reply. >> >> I'm following the tutorial. >> >> > Please clarify whether you're using Anirban's or mine. Now that two > exist, people will have to be a fair bit more specific :) > > > In your system, to solvate it you have the values that was used during the >> protien insertion into the bilayer. Following it, I have used the >> following >> commandfor my system where the protein is very much smaller than the >> length >> of the bilayer. >> >> $ editconf -f shrinked4.gro -o shrinked4_1.gro -box 6.41840 6.44350 >> 6.59650 >> >> $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top >> >> > If you have to manipulate the box of any coordinate file produced by > InflateGRO, whatever you're doing is wrong. You should not be solvating > anything until the very last step of the procedure, where your bilayer is > of correct size and APL. Exactly, solvate at the end of all the compression steps performed by InflateGro (may be 10 or 20 depending on your system) and minimizations (of only protein + lipid) until you have reached the correct area per lipid. And then only solvate. Check for the dimensions in the last line of the FINAL (compressed and minimized) .gro file and then solvate Thanks, Anirban > > > But I could see in the visualizer that SOL molecules were added on top and >> bottom but only 1/3 of the length of the bilayer. >> How to add SOL molecules to whole length or how to remove not-solvated >> part >> of lipids? >> >> > This outcome is a consequence of re-adjusting the box size of a system > that likely has other dimensions. As far as I can tell, you shouldn't be > doing this. > > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 3:27 PM, Bala S wrote: > Thank you for that clarification. > > I found that there were SOL molecules in .top file. I could run the EM now. > > Coming to the Solvation step, I'm facing a problem. > > I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat > locally. > > While adding the solvent molecules, what command should I be using? > > I am using the usual command I use for non-membrane simulations, > > $ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic > > followed by > > $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top > When you mention -bt cubic, it adds a cubic water box all around your system (if you visualize you will see your entire bilayer immersed in a cubic water box like a normal protein solvation). But that is wrong. You need to add water only on either side of the lipid membrane (that is along the z-axis only). So use the -box option with editconf without using -c and -d. You can have a look at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial It is clearly mentioned over there how to go about it. > > calculation goes for long time showing a huge number of SOL molecules. > > I guess I'm worng somehere. > > Thanks. > > Bala S > > > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding errors
On Fri, Apr 27, 2012 at 3:17 PM, seera suryanarayana wrote: > Respected Sir, > > While i am running gromacs software i am getting the > following error.Kindly knowing me how to over come the error. > > Fatal error: > number of coordinates in coordinate > file (1cys_ion.gro, 99670) > does not match topology (1cys.top, > 99680) > > Your .top file contains 10 extra atoms than you .gro file. Check whether any ion has been mentioned twice by mistake in the .top file. > > > SURYANARAYANA SEERA, > PhD student. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
On Fri, Apr 27, 2012 at 1:01 PM, Bala S wrote: > Dear Justin > > Thanks for the explanation. > > I am following your tutorial of KALP membrane simulation. I am stuck in > between two steps of InflateGRO. After the first step, the tutorial > requests > to perform EM. Should I be running grompp with new system_inflated.gro file > to generate a new .tpr file for EM or should I perform EM with em.tpr > which was generated some time back in the tutorial? You should run grompp with the inflated .gro file (system_inflated.gro) since you will be minimizing the inflated .gro file after every compression step to remove bad contacts. The earlier em.tpr was used to remove periodicity of the bilayer only. > The latter ran EM but the > former shows error 'number of coordinates in coordinate file > (system_inflated.gro, 6438) > does not match topology (topol.top, 17403)" > The difference in atom numbers might be because your .top file contains some extra molecules in the [ molecules ] section (may be SOL). Use .top file that contains only protein and lipid molecules. > Thanks. > > Bala S > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933137.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)
Hello Bala, Yes, exactly as Justin said it represents just a workflow where a GPCR protein (here B2AR) has been taken as an example. I mentioned it as a GPCR tutorial because many often inquire about GPCR MD simulations only in the forum. But it can be adapted for other membrane proteins as well. And secondly again as Justin mentioned, the choice of lipid depends upon the system you wish to replicate. Regards, Anirban On Thu, Apr 26, 2012 at 11:10 PM, Justin A. Lemkul wrote: > > > On 4/26/12 9:35 AM, Bala S wrote: > >> Dear Anirban, >> >> Thanks for the tutorial you have created for the newbies like me to >> follow. >> >> I wonder the tutorial is only for the GPCRs not applicable for other >> membrane proteins? >> >> > Tutorials present possible workflows. Anirban's tutorial does not > significantly differ from my own (linked from his) which I happen to know > has been applied to many different systems. There is nothing GPCR-specific > in this new tutorial, just like there is nothing KALP-specific about mine. > > > I also have another question about slecting a lipidbilayer, what is the >> criteria is selecting it, for instance popc, dopc or dppc? >> >> > The choice of lipid depends on what you need to model. > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, On our cluster I usually get around 25-30 ns/day running on 120 cores (system size around 85K atoms) with PME. Regards, Anirban On Thu, Apr 26, 2012 at 5:28 PM, Albert wrote: > Hi Anirban: > how many ns/day for your simulations? Did you use PME? > > best > Albert > > > > On 04/26/2012 12:59 PM, Anirban Ghosh wrote: > >> Hello Albert, >> >> Good to know that! >> I have carried out simulations using this FF in the range of 600 ns. >> >> Regards, >> >> Anirban >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban On Thu, Apr 26, 2012 at 3:47 PM, Albert wrote: > Hello Anirban: > > thanks for kind comments. > How long did you mean " fairly long simulation time" ? does 1u ns belongs > to this range? CHARMM36 ff is available in gromacs website and we can > download it and put them into top directory and then it works. It is not > need to make any modification by ourselves. > > best > Albert > > > > On 04/26/2012 11:53 AM, Anirban Ghosh wrote: > >> Hello Albert, >> >> Thanks. >> Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS >> 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very >> well preserves the characters of both the protein as well as the lipids for >> fairly long simulation time, hence I used that FF in the tutorial. But one >> can surely add CHARMM36 to GROAMCS by doing all the necessary topology >> conversions. >> >> >> Regards, >> >> Anirban >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)
Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the protein as well as the lipids for fairly long simulation time, hence I used that FF in the tutorial. But one can surely add CHARMM36 to GROAMCS by doing all the necessary topology conversions. Regards, Anirban On Thu, Apr 26, 2012 at 3:08 PM, Albert wrote: > it seesm to be good. > just one pieces of advices, why not use CHARMM36 for this tutorial ? since > it is the best FF for lipids currently. > > > On 04/26/2012 11:14 AM, Anirban Ghosh wrote: > > Hi ALL, > > I have prepared a step-wise tutorial for running a MD simulation of a > GPCR protein inserted in a lipid bilayer. It can be found at the following > URL: > > https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial > > I sincerely hope it will help people who are new to such simulations and > the GROMACS community in general. This tutorial is adapted from the > membrane protein tutorial prepared by Justin Lemkul. > > > Regards, > > Anirban > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GPCR MD Tutorial Using GROMACS (URL)
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GPCR MD Tutorial Using GROMACS
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. It can be found at the following URL: https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GPCR MD Tutorial Using GROMACS
Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid bilayer. I sincerely hope it will help people who are new to such simulations and the GROMACS community in general. This tutorial is adapted from the membrane protein tutorial prepared by Justin Lemkul. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Best Force Field for a Membrane Protein
Hi ALL, Thanks a lot for the replies. By long simulation I mean 500 ns to 1000 ns. Has anybody tried with the ff43a1 with any membrane protein? Thanks, Anirban On Fri, Apr 20, 2012 at 3:26 AM, Peter C. Lai wrote: > Define long simulations? CHARMM27/36 in the sub-100ns timescale works for > us. > > The following paper: > Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting > Novel Binding Modes of > Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics > Simulations. PLoS > Comput Biol 7, e1001053 (2011) > > Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system. > > On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote: > > Hi ALL, > > > > When running a membrane protein (say GPCR) in a lipid bilayer (say POPC > or > > DPPC etc.) which according to your experience is the most suited > > force-field in GROMACS that best retains the 7TM / secondary structures > of > > the protein over long simulations? I have tried running with ff53a6 (as > > suggested in Justin's tutorial), but find that the helices in the bilayer > > tend to lose their helicity over time and turns into coils. ff43a2 seems > to > > do the job somewhat better by retaining the helicity. Will ff43a1 work > even > > better as the principle aim is to observe changes in the protein without > > losing its secondary structures? Your experience please. > > Thanks a lot in advance. > > > > > > Regards, > > > > Anirban > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > == > Peter C. Lai| University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > == > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Best Force Field for a Membrane Protein
Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Membrane Proteins & pdb2gmx
Hello Peter, Thanks a lot for clarifying my doubt! I have got it right now. Thanks, Anirban On Thu, Dec 8, 2011 at 3:34 PM, Peter C. Lai wrote: > On 2011-12-08 02:43:13AM -0600, Anirban Ghosh wrote: > > Hello Justin, > > > > In your membrane protein simulation tutorial after making the topology, > you have mentioned that "Placing the new gromos53a6_lipid.ff directory in > $GMXLIB will allow you to use this force field system-wide." I suppose this > is valid only for the proteins (and not membranes) to be processed through > pdb2gmx using gromos53a6_lipid force-field, right? And to process a > membrane using pdb2gmx we need to change the aminoacids.rtp file with the > relevent POPC/DSPC/DPPC etc. entries. Right? Or can we somehow make pdb2gmx > use the POPC/DPPC/DSPC.itp file? > > Yes because in that tutorial, you are not adding an rtp with the lipid > residue names to generate lipid topologies "from scratch". The tutorial > uses pregenerated lipid topologies from Tieleman. You are certainly > able to add your own rtp files; pdb2gmx searches all validly formatted > rtp files in $GMXLIB/forcefield.ff/ for topology information by residue > name. For example, when I converted parts of CGenFF to gromacs, I added > my own library of residue types for the small molecules I am modeling as > its own .rtp file. (Basically what I mean is, there is no need to hack > aminoacids.rtp to add new residues, just add your own .rtp file). > > However you obtain a topology of a moleculetype (either using pdb2gmx or > from someone else e.g. Tieleman) with a given forcefield, you do not need > to > run pdb2gmx again to generate another topology using that forcefield for > subsequent tasks. Just include the relevant .itp file in the .top file > you specify to grompp. For example, I generated POPC.itp once and have been > using the same file for all my simulations involving POPC. > > Here is an entire membrane protein+lipid+water+ligand .top ready for > grompp -p (I use charmm36 with cgenff added - this is analogous to Justin's > gromos53a6_lipid modification): > > > #include "charmm36cgen.ff/forcefield.itp" > #include "gpcr.itp" > #include "popc.itp" > #include "charmm36cgen.ff/tips3p.itp" > #include "charmm36cgen.ff/ions.itp" > #include "ligand.itp" > > [ system ] > ; Name > GPCR in POPC with LIGAND > > [ molecules ] > GPCR 1 > ; the gpcr.itp file starts with: > ; [ moleculetype ] > ; ; Namenrexcl > ; GPCR 3 > POPC 230 > SOL 21468 > NA 2 > LIGAND 1 > > > gpcr.itp, popc.itp, and ligand.itp were all originally generated by me > using > pdb2gmx on the relevant molecules coordinate files at one point or another. > Again, these individual .itp files are reusable for other simulations > involving the same molecule types, protonation states, and charmm36cgen.ff. > > Hope that helps. > > -- > == > Peter C. Lai| University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > == > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Membrane Proteins & pdb2gmx
Hello Justin, In your membrane protein simulation tutorial after making the topology, you have mentioned that "Placing the new gromos53a6_lipid.ff directory in $GMXLIB will allow you to use this force field system-wide." I suppose this is valid only for the proteins (and not membranes) to be processed through pdb2gmx using gromos53a6_lipid force-field, right? And to process a membrane using pdb2gmx we need to change the aminoacids.rtp file with the relevent POPC/DSPC/DPPC etc. entries. Right? Or can we somehow make pdb2gmx use the POPC/DPPC/DSPC.itp file? Thanks a lot. Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CPHMD in GROMACS4.5
Hi ALL, Is it possible to run constant pH MD simulation (CPHMD) in Gromacs4.5? Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rdf query
Hi ALL, I am using in calculating the distribution of a solvent around the COM of a protein chain using g_rdf. When I plot the output file (attached) I get a curve which increases first (from 1 to a value of about 2.5) and then decreases to x-axis values ranging from 1 to 5. If I understand correctly then x-axis values represent the radius of calculation around the protein. right? It says "r". Whats its unit? And what does the y-axis values stand for? Can someone please explain me the g_rdf plot attached here. Thanks a lot in advance. Regards, Anirban <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GridMatMD and CGMD
Hello Justin, Thanks for the reply. Actually I am using the last frame .gro of a 3 micro-second run CGMD simulation as the input for GridMatMD. But in the thickness plot the positions of the protein depicted are not matching with what I am visualizing through VMD. I suppose this is because of some PBC issue. What -pbc options should I use to generate a proper .gro file to be used as input for GridMatMD? Thanks a lot again. Regards, Anirban On Mon, May 30, 2011 at 4:40 PM, Justin A. Lemkul wrote: > > Anirban Ghosh wrote: > >> Hi ALL, >> >> I have simulated a CGMD system consisting of multiple copies of a CG >> protein in a CG lipid bilayer using the MARTINI FF for the CG definitions. >> Can I use GridMatMD program to calculate the area per lipid and other >> properties in this CG system? Which parameters do I need to alter in the >> input file for GridMatMD in order to properly recognize the CG lipids? >> > > CG lipids should work like any other - specify their name in the input > file, and the atom name that should be used as a reference point. We have > never tested GridMAT-MD with a CG membrane, but it should work the same way > as an atomistic membrane. Please let me know if you encounter any problems. > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GridMatMD and CGMD
Hi ALL, I have simulated a CGMD system consisting of multiple copies of a CG protein in a CG lipid bilayer using the MARTINI FF for the CG definitions. Can I use GridMatMD program to calculate the area per lipid and other properties in this CG system? Which parameters do I need to alter in the input file for GridMatMD in order to properly recognize the CG lipids? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About -pbc option of trjconv
Hi ALL, I have a long simulation trajectory of 3 micro-seconds of multiple protein monomers in a lipid bilayer. Which -pbc option should be used with trjconv to process the trajectory before carrying out any analysis? I am using -pbc nojump, is it correct? Or should I use -pbc whole? Thanks a lot in advance. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_msd query
Hi ALL, I am trying to calculate the lateral diffusion coefficient of a protein in a bilayer (CG simulation using MARTINI FF). The simulation length is 5 micro-seconds. I wanted to know based on what should i set the values of -beginfit and -endfit and also the value for -trestart. Is it necessary to set -trestart? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_sas query
Hello Tsjerk & Mark, Thanks for the reply. Actually more important than the ions is the lipid bilayer of my system. Actually my protein is a GPCR embedded in a lipid bilayer. So when I want to calculate the SASA of my protein, so should I use a group (Protein+Lipid+Ions) as the calculation group and Protein as the output group? Thanks again, Anirban On Sat, May 7, 2011 at 1:05 PM, Mark Abraham wrote: > On 7/05/2011 4:36 PM, Anirban Ghosh wrote: > > Hello Tsjerk, > > Thanks for the reply. > But if I consider the ions also in the calculation group, then it is not > wrong. Right? > > > Only you know where your ions are, and whether their contribution to > surface area means anything. Make the hybrid groups accordingly. > > Mark > > > Thanks, > > Anirban > > On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar wrote: > >> Hey Anirban, >> >> I would consider the ions part of the solvent. But the procedure is right. >> >> Cheers, >> >> Tsjerk >> >> On May 7, 2011 7:35 AM, "Anirban Ghosh" >> wrote: >> >> Hi ALL, >> >> I want to calculate the SASA of a protein embedded in a bilayer along >> with water and ions. So while using g_sas I understand that I need to supply >> all non-solvent atoms as calculation group and Protein as the output group. >> So I need to make a group with Protein+Lipid+Ions as the calculation group. >> Right? >> Thanks a lot in advance. >> >> Regards, >> >> Anirban >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_sas query
Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar wrote: > Hey Anirban, > > I would consider the ions part of the solvent. But the procedure is right. > > Cheers, > > Tsjerk > > On May 7, 2011 7:35 AM, "Anirban Ghosh" > wrote: > > Hi ALL, > > I want to calculate the SASA of a protein embedded in a bilayer along with > water and ions. So while using g_sas I understand that I need to supply all > non-solvent atoms as calculation group and Protein as the output group. So I > need to make a group with Protein+Lipid+Ions as the calculation group. > Right? > Thanks a lot in advance. > > Regards, > > Anirban > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_sas query
Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat error of different spacing
Hello Justin, I am using Gromacs 4.0.7 Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining. So what should i do? Thanks, Anirban On Thu, May 5, 2011 at 7:58 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Hello Justin, >> >> Thanks for the reply. >> gmxcheck on the first trajectory shows: >> >> >> - >> Checking file protein_3000NS_2.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time 2957280.000 # Atoms 57296 >> Reading frame1400 time 2999280.000 >> Item#frames Timestep (ps) >> Step 142530 >> Time 142530 >> Lambda142530 >> Coords142530 >> Velocities142530 >> Forces 0 >> Box 142530 >> >> --- >> >> And on the second trajectory shows: >> >> >> --- >> Checking file B2AR_self_assembly_3500NS.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time 300.000 # Atoms 57296 >> Reading frame 16000 time 348.000 >> Item#frames Timestep (ps) >> Step 1666730 >> Time 1666730 >> Lambda 1666730 >> Coords 1666730 >> Velocities 1666730 >> Forces 0 >> Box 1666730 >> >> --- >> >> So gmxcheck does not show any warning/error. >> Then why I am getting the warning from trjcat. And how to remove it? >> >> > I don't know yet. A few more questions: > > 1. What version of Gromacs are you using? > > 2. How many total trajectories are you concatenating? You said there was a > problem from 10 -> 300 ns, but I don't see any times shown here below > 2957280. The real problem could be early on in the trajectory. > > -Justin > > Thanks, >> >> Anirban >> >> >> On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Anirban Ghosh wrote: >> >> >>Hi ALL, >> >>I am trying to use trjcat -f input files -o output_file to join >>to very larger trajectories. However I am getting the following >>error: >> >> >> >> --- >>Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 >>ps, frame=98576 -> frame 10 time 300.000 ps -> >> frame 99980 time 2999400.000 psWARNING: Frames around >>t=300.00 ps have a different spacing than the rest, >>might be a gap or overlap that couldn't be corrected automatically. >>Reading frame 0 time 390.000 lasttime 3e+06 >> >>Continue writing frames from protein_4000NS.trr t=3.9e+06 >>ps, frame=11 >> >> --- >> >>And if I use this resultant output trajectory for further >>analysis like g_sas, then a portion between around 10 ns and >>300 ns is simply joined by a straight line. >>How to remove this inconsistency from the two trajectories? >>Any suggestion is welcome. >> >> >>What does gmxcheck tell you about each of the individual >>trajectories (prior to running trjcat)? >> >>-Justin >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.o
Re: [gmx-users] trjcat error of different spacing
Hello Justin, Thanks for the reply. gmxcheck on the first trajectory shows: - Checking file protein_3000NS_2.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 2957280.000 # Atoms 57296 Reading frame1400 time 2999280.000 Item#frames Timestep (ps) Step 142530 Time 142530 Lambda142530 Coords142530 Velocities142530 Forces 0 Box 142530 --- And on the second trajectory shows: --- Checking file B2AR_self_assembly_3500NS.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 300.000 # Atoms 57296 Reading frame 16000 time 348.000 Item#frames Timestep (ps) Step 1666730 Time 1666730 Lambda 1666730 Coords 1666730 Velocities 1666730 Forces 0 Box 1666730 --- So gmxcheck does not show any warning/error. Then why I am getting the warning from trjcat. And how to remove it? Thanks, Anirban On Thu, May 5, 2011 at 7:19 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> >> Hi ALL, >> >> I am trying to use trjcat -f input files -o output_file to join to very >> larger trajectories. However I am getting the following error: >> >> >> --- >> Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, >> frame=98576 -> frame 10 time 300.000 ps -> frame 99980 >> time 2999400.000 psWARNING: Frames around t=300.00 ps have a >> different spacing than the rest, >> might be a gap or overlap that couldn't be corrected automatically. >> Reading frame 0 time 390.000 lasttime 3e+06 >> >> Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, >> frame=11 >> --- >> >> And if I use this resultant output trajectory for further analysis like >> g_sas, then a portion between around 10 ns and 300 ns is simply joined >> by a straight line. >> How to remove this inconsistency from the two trajectories? >> Any suggestion is welcome. >> > > What does gmxcheck tell you about each of the individual trajectories > (prior to running trjcat)? > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjcat error of different spacing
Hi ALL, I am trying to use trjcat -f input files -o output_file to join to very larger trajectories. However I am getting the following error: --- Continue writing frames from protein_3000NS_2.trr t=2.95728e+06 ps, frame=98576 -> frame 10 time 300.000 ps -> frame 99980 time 2999400.000 ps WARNING: Frames around t=300.00 ps have a different spacing than the rest, might be a gap or overlap that couldn't be corrected automatically. Reading frame 0 time 390.000 lasttime 3e+06 Continue writing frames from protein_4000NS.trr t=3.9e+06 ps, frame=11 --- And if I use this resultant output trajectory for further analysis like g_sas, then a portion between around 10 ns and 300 ns is simply joined by a straight line. How to remove this inconsistency from the two trajectories? Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CG to FG transformation error
Hi, I have successfully converted my CG (only) protein model to FG model using g_fg2cg command of the gromacs_reverse package. But now when I try to compile my .mdp file for SA run, grompp is throwing some warnings: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# WARNING 1 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_force' in parameter file WARNING 2 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_a' in parameter file WARNING 3 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restr' in parameter file WARNING 4 [file fg_protein.mdp, line unknown]: Unknown left-hand 'r_CGW' in parameter file WARNING 5 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... processing topology... - My system contains only multiple copies of a protein. How to solve this issue? Any suggestion is welcome. Thanks, -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error: No such moleculetype Protein
Hi, I have worked around the problem. I was not including a .itp file. But now I am getting Segmentation Fault: Excluding 1 bonded neighbours for DSPC 104 Excluding 1 bonded neighbours for W 1397 Excluding 1 bonded neighbours for NA+ 0 Excluding 1 bonded neighbours for CL- 4 Number of fg atoms 410288 Number of cg atoms 57296 Reading frames from gro file 'Protein in DSPC Bilayer', 57296 atoms. Reading frame 0 time0.000 1297343010 Segmentation fault Why is this happening? Thanks, Anirban On Thu, Feb 10, 2011 at 5:45 PM, Anirban Ghosh < reach.anirban.gh...@gmail.com> wrote: > Hi Tsjerk, > > Thanks for the reply. > Yes, I had a reference to 'Protein' group in my .mdp file while running the > CGMD. Now, after CG run I am trying to convert the CG to FG model using: > > g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro > > So do I need to supply any other parameter to this command or how to > mention this refering of 'Protein' group here. > > Thanks, > > Anirban > > > > On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar wrote: > >> Hi Anirban, >> >> Probably you have a reference to a group 'Protein' in your .mdp file. >> >> Cheers, >> >> Tsjerk >> >> On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh >> wrote: >> > Hi, >> > I am trying to convert a CG system containing multiple copies of a >> protein + >> > lipid + water + ions to an all-atom system using the special >> gromacs_reverse >> > version command g_fg2cg. However I am getting the error: >> > >> --- >> > calling cpp... >> > processing topology... >> > Generated 4 of the 780 non-bonded parameter combinations >> > Cleaning up temporary file grompp9YJMaA >> > --- >> > Program g_fg2cg, VERSION 3.3.1 >> > Source code file: ../kernel/toppush.c, line: 1293 >> > Fatal error: >> > No such moleculetype Protein >> > >> - >> > I have checked all the include statements and .itp files, but cannot fix >> the >> > issue. Is seems to be very trivial but still exists. >> > Any suggestion is welcome. >> > >> > Thanks, >> > Anirban >> > -- >> > gmx-users mailing listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error: No such moleculetype Protein
Hi Tsjerk, Thanks for the reply. Yes, I had a reference to 'Protein' group in my .mdp file while running the CGMD. Now, after CG run I am trying to convert the CG to FG model using: g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro So do I need to supply any other parameter to this command or how to mention this refering of 'Protein' group here. Thanks, Anirban On Thu, Feb 10, 2011 at 5:28 PM, Tsjerk Wassenaar wrote: > Hi Anirban, > > Probably you have a reference to a group 'Protein' in your .mdp file. > > Cheers, > > Tsjerk > > On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh > wrote: > > Hi, > > I am trying to convert a CG system containing multiple copies of a > protein + > > lipid + water + ions to an all-atom system using the special > gromacs_reverse > > version command g_fg2cg. However I am getting the error: > > > --- > > calling cpp... > > processing topology... > > Generated 4 of the 780 non-bonded parameter combinations > > Cleaning up temporary file grompp9YJMaA > > --- > > Program g_fg2cg, VERSION 3.3.1 > > Source code file: ../kernel/toppush.c, line: 1293 > > Fatal error: > > No such moleculetype Protein > > > - > > I have checked all the include statements and .itp files, but cannot fix > the > > issue. Is seems to be very trivial but still exists. > > Any suggestion is welcome. > > > > Thanks, > > Anirban > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error: No such moleculetype Protein
Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --- calling cpp... processing topology... Generated 4 of the 780 non-bonded parameter combinations Cleaning up temporary file grompp9YJMaA --- Program g_fg2cg, VERSION 3.3.1 Source code file: ../kernel/toppush.c, line: 1293 Fatal error: No such moleculetype Protein - I have checked all the include statements and .itp files, but cannot fix the issue. Is seems to be very trivial but still exists. Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] DSPC all atom .itp file
Hi ALL, Can anyone please send me an all-atom DSPC .itp file at * reach.anirban.gh...@gmail.com *or* anirba...@gmail.com* * * Thanks a lot. -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CG to FG transformation error
Hi, I am trying to convert a coarse grained protein to a full atom model after CGMD. I am using the modified gromacs_reverse code available from MARTINI site. I am using the following command: g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro But in the output full.gro all the atoms are having coordinate values as "0.00". My pro_cg.top file looks like: #define _FF_GROMOS96 #define _FF_GROMOS42A2 ;#define _FF_GROMACS ;#define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.125 0.5 #include "ffG43a2nb.itp" #include "ffG43a2bon.itp" Is this correct? where I am going wrong? I think the problem is with pro_cg.top file only. Any suggestion is welcome. Thanks, -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] DSPC all atom .itp file
Hi ALL, Can anyone please send me an all-atom DSPC .itp file at * reach.anirban.gh...@gmail.com *or* anirba...@gmail.com* * * Thanks a lot. -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_lie query
Thanks Justin. Yes I did use PME during the simulations. But still when I process the .edr file with g_energy, it gives both the options...LJ-1-4 and LJ(SR). So if I am not wrong, I should be using the LJ(SR) value as the Elj in the LIE calculation. Right? Thanks again. Anirban On Tue, Dec 28, 2010 at 11:45 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Thanks a lot Justin for the reply !!! >> >> While calculating the Elj and Eqq values should we consider the >> short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in >> > > 1-4 interactions are intramolecular, thus should not be relevant to the LIE > calculation. > > > the .edr file? And for Coulomb also? >> Which one should we consider? >> > > Did you use PME? If so, you can't break down the Coulombic terms entirely. > > -Justin > > >> Thanks again. >> >> Anirban >> >> >> >> On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Anirban Ghosh wrote: >> >>Thanks a lot Justin for the reply. >>Yes I am going through all the relevant literature on LIE. >>Actually the lie.xvg file contains the same value of -25.4 for >>all the frames. So I am getting a straight line plot. Why is >>this happening? Am I missing out something? >> >> >>If the interactions of your ligand and its receptor are stable, then >>there may be no change in the energetics. I don't know anything >>about your system, so I can't say anything beyond that. >> >>-Justin >> >>Thanks a lot again. >> >>Anirban >> >> >>On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Thanks a lot Justin for the reply. >> So I ran a simulation with my ligand in water for 1 ns >>and using >> g_energy I calculated the LG-14 and Coulomb-14 values >>from the >> .edr file. I supplied the average of these two values as >>my Elj >> and Eqq to g_lie and I got the DGbind as -25.4. Is this the >> correct way to do this? >> >> >> Again I would ask you to not rely entirely upon my advice for >>this. >>I have only examined the LIE method sparingly. My best >>answer is, >> "probably," but do read the literature on the method to be sure. >> >> >> And why am I getting only a single value of DGbind for >>all the >> frames captured in the .edr file? >> >> >> The lie.xvg file contains the LIE values as a function of time. >> What's printed to the screen is the average value and standard >> deviation. >> >> -Justin >> >> Thanks a lot. >> >> Anirban >> >> >> On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul >> mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Thanks Justin for the reply. >> I have through the threads about g_lie, but cannot >>understand >> how to get the values for Elj and Eqq for a >> particular >> ligand. >> Like in my case for a system consisting of a beta2AR >> protein + >> dopamine (ligand) + POPC + water, what should be the >> values for >> Elj and Eqq? >> >> >> To obtain these (from my limited understanding), you >> would >> have to >> run a simulation of your ligand in water, decomposing the >> nonbonded >> energies between the ligand and solvent into LJ and >>Coulombic >> components. Those are your values. >> &g
Re: [gmx-users] g_lie query
Thanks a lot Justin for the reply !!! While calculating the Elj and Eqq values should we consider the short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in the .edr file? And for Coulomb also? Which one should we consider? Thanks again. Anirban On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Thanks a lot Justin for the reply. >> Yes I am going through all the relevant literature on LIE. >> Actually the lie.xvg file contains the same value of -25.4 for all the >> frames. So I am getting a straight line plot. Why is this happening? Am I >> missing out something? >> >> > If the interactions of your ligand and its receptor are stable, then there > may be no change in the energetics. I don't know anything about your > system, so I can't say anything beyond that. > > -Justin > > Thanks a lot again. >> >> Anirban >> >> >> On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Anirban Ghosh wrote: >> >>Thanks a lot Justin for the reply. >>So I ran a simulation with my ligand in water for 1 ns and using >>g_energy I calculated the LG-14 and Coulomb-14 values from the >>.edr file. I supplied the average of these two values as my Elj >>and Eqq to g_lie and I got the DGbind as -25.4. Is this the >>correct way to do this? >> >> >>Again I would ask you to not rely entirely upon my advice for this. >> I have only examined the LIE method sparingly. My best answer is, >>"probably," but do read the literature on the method to be sure. >> >> >>And why am I getting only a single value of DGbind for all the >>frames captured in the .edr file? >> >> >>The lie.xvg file contains the LIE values as a function of time. >> What's printed to the screen is the average value and standard >>deviation. >> >>-Justin >> >>Thanks a lot. >> >>Anirban >> >> >>On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Thanks Justin for the reply. >> I have through the threads about g_lie, but cannot >> understand >> how to get the values for Elj and Eqq for a particular >>ligand. >> Like in my case for a system consisting of a beta2AR >>protein + >> dopamine (ligand) + POPC + water, what should be the >>values for >> Elj and Eqq? >> >> >> To obtain these (from my limited understanding), you would >>have to >> run a simulation of your ligand in water, decomposing the >>nonbonded >> energies between the ligand and solvent into LJ and Coulombic >> components. Those are your values. >> >> I should also note that simply going through the archive to >>inform >> yourself about the LIE method is insufficient. The original >> literature, and several subsequent papers (one at least >>within the >> last year, IIRC), describes the accuracy of the method and >>what it >> needs to be properly run. >> >> -Justin >> >> Thanks a lot. >> >> Anirban >> On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul >> mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Hi ALL, >> >> I have run a protein + ligand (dopamine) >>simulation. Now >> I want >> to calculate the free energy of binding using >>g_lie. But >> g_lie >> asks for two values: Elj and Eqq. How or from >>where can I get >> these va
Re: [gmx-users] g_lie query
Thanks a lot Justin !!! --Anirban On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Thanks a lot Justin for the reply. >> Yes I am going through all the relevant literature on LIE. >> Actually the lie.xvg file contains the same value of -25.4 for all the >> frames. So I am getting a straight line plot. Why is this happening? Am I >> missing out something? >> >> > If the interactions of your ligand and its receptor are stable, then there > may be no change in the energetics. I don't know anything about your > system, so I can't say anything beyond that. > > -Justin > > Thanks a lot again. >> >> Anirban >> >> >> On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Anirban Ghosh wrote: >> >>Thanks a lot Justin for the reply. >>So I ran a simulation with my ligand in water for 1 ns and using >>g_energy I calculated the LG-14 and Coulomb-14 values from the >>.edr file. I supplied the average of these two values as my Elj >>and Eqq to g_lie and I got the DGbind as -25.4. Is this the >>correct way to do this? >> >> >>Again I would ask you to not rely entirely upon my advice for this. >> I have only examined the LIE method sparingly. My best answer is, >>"probably," but do read the literature on the method to be sure. >> >> >>And why am I getting only a single value of DGbind for all the >>frames captured in the .edr file? >> >> >>The lie.xvg file contains the LIE values as a function of time. >> What's printed to the screen is the average value and standard >>deviation. >> >>-Justin >> >>Thanks a lot. >> >>Anirban >> >> >>On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Thanks Justin for the reply. >> I have through the threads about g_lie, but cannot >> understand >> how to get the values for Elj and Eqq for a particular >>ligand. >> Like in my case for a system consisting of a beta2AR >>protein + >> dopamine (ligand) + POPC + water, what should be the >>values for >> Elj and Eqq? >> >> >> To obtain these (from my limited understanding), you would >>have to >> run a simulation of your ligand in water, decomposing the >>nonbonded >> energies between the ligand and solvent into LJ and Coulombic >> components. Those are your values. >> >> I should also note that simply going through the archive to >>inform >> yourself about the LIE method is insufficient. The original >> literature, and several subsequent papers (one at least >>within the >> last year, IIRC), describes the accuracy of the method and >>what it >> needs to be properly run. >> >> -Justin >> >> Thanks a lot. >> >> Anirban >> On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul >> mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Hi ALL, >> >> I have run a protein + ligand (dopamine) >>simulation. Now >> I want >> to calculate the free energy of binding using >>g_lie. But >> g_lie >> asks for two values: Elj and Eqq. How or from >>where can I get >> these values for my ligand? Also, do I need to run a >> simulation >> with only the ligand? And, is there any other way >>(like >> MMGBSA >> in Amber) to calculate the free energy for my >>simulation?
Re: [gmx-users] g_lie query
Thanks a lot Justin for the reply. Yes I am going through all the relevant literature on LIE. Actually the lie.xvg file contains the same value of -25.4 for all the frames. So I am getting a straight line plot. Why is this happening? Am I missing out something? Thanks a lot again. Anirban On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Thanks a lot Justin for the reply. >> So I ran a simulation with my ligand in water for 1 ns and using g_energy >> I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied >> the average of these two values as my Elj and Eqq to g_lie and I got the >> DGbind as -25.4. Is this the correct way to do this? >> > > Again I would ask you to not rely entirely upon my advice for this. I have > only examined the LIE method sparingly. My best answer is, "probably," but > do read the literature on the method to be sure. > > > And why am I getting only a single value of DGbind for all the frames >> captured in the .edr file? >> >> > The lie.xvg file contains the LIE values as a function of time. What's > printed to the screen is the average value and standard deviation. > > -Justin > > Thanks a lot. >> >> Anirban >> >> >> On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Anirban Ghosh wrote: >> >>Thanks Justin for the reply. >>I have through the threads about g_lie, but cannot understand >>how to get the values for Elj and Eqq for a particular ligand. >>Like in my case for a system consisting of a beta2AR protein + >>dopamine (ligand) + POPC + water, what should be the values for >>Elj and Eqq? >> >> >>To obtain these (from my limited understanding), you would have to >>run a simulation of your ligand in water, decomposing the nonbonded >>energies between the ligand and solvent into LJ and Coulombic >>components. Those are your values. >> >>I should also note that simply going through the archive to inform >>yourself about the LIE method is insufficient. The original >>literature, and several subsequent papers (one at least within the >>last year, IIRC), describes the accuracy of the method and what it >>needs to be properly run. >> >>-Justin >> >>Thanks a lot. >> >>Anirban >>On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Hi ALL, >> >> I have run a protein + ligand (dopamine) simulation. Now >>I want >> to calculate the free energy of binding using g_lie. But >>g_lie >> asks for two values: Elj and Eqq. How or from where can I >> get >> these values for my ligand? Also, do I need to run a >>simulation >> with only the ligand? And, is there any other way (like >>MMGBSA >> in Amber) to calculate the free energy for my simulation? >> Any >> suggestion is welcome. >> Thanks a lot in advance. >> >> >> Go to the literature and understand what information is >>needed for >> such a simulation, and then look into the list archives and >>you'll >> find dozens of threads about using g_lie. >> >> -Justin >> >> >> Regards, >> >> Anirban >> >> >> -- >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >>231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >>
Re: [gmx-users] g_lie query
Thanks a lot Justin for the reply. So I ran a simulation with my ligand in water for 1 ns and using g_energy I calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied the average of these two values as my Elj and Eqq to g_lie and I got the DGbind as -25.4. Is this the correct way to do this? And why am I getting only a single value of DGbind for all the frames captured in the .edr file? Thanks a lot. Anirban On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Thanks Justin for the reply. >> I have through the threads about g_lie, but cannot understand how to get >> the values for Elj and Eqq for a particular ligand. Like in my case for a >> system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, >> what should be the values for Elj and Eqq? >> >> > To obtain these (from my limited understanding), you would have to run a > simulation of your ligand in water, decomposing the nonbonded energies > between the ligand and solvent into LJ and Coulombic components. Those are > your values. > > I should also note that simply going through the archive to inform yourself > about the LIE method is insufficient. The original literature, and several > subsequent papers (one at least within the last year, IIRC), describes the > accuracy of the method and what it needs to be properly run. > > -Justin > > Thanks a lot. >> >> Anirban >> On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Anirban Ghosh wrote: >> >>Hi ALL, >> >>I have run a protein + ligand (dopamine) simulation. Now I want >>to calculate the free energy of binding using g_lie. But g_lie >>asks for two values: Elj and Eqq. How or from where can I get >>these values for my ligand? Also, do I need to run a simulation >>with only the ligand? And, is there any other way (like MMGBSA >>in Amber) to calculate the free energy for my simulation? Any >>suggestion is welcome. >>Thanks a lot in advance. >> >> >>Go to the literature and understand what information is needed for >>such a simulation, and then look into the list archives and you'll >>find dozens of threads about using g_lie. >> >>-Justin >> >> >>Regards, >> >>Anirban >> >> >>-- >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >>http://lists.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before >>posting! >>Please don't post (un)subscribe requests to the list. Use the www >>interface or send it to gmx-users-requ...@gromacs.org >><mailto:gmx-users-requ...@gromacs.org>. >> >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_lie query
Thanks Justin for the reply. I have through the threads about g_lie, but cannot understand how to get the values for Elj and Eqq for a particular ligand. Like in my case for a system consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what should be the values for Elj and Eqq? Thanks a lot. Anirban On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Hi ALL, >> >> I have run a protein + ligand (dopamine) simulation. Now I want to >> calculate the free energy of binding using g_lie. But g_lie asks for two >> values: Elj and Eqq. How or from where can I get these values for my ligand? >> Also, do I need to run a simulation with only the ligand? And, is there any >> other way (like MMGBSA in Amber) to calculate the free energy for my >> simulation? Any suggestion is welcome. >> Thanks a lot in advance. >> >> > Go to the literature and understand what information is needed for such a > simulation, and then look into the list archives and you'll find dozens of > threads about using g_lie. > > -Justin > > >> Regards, >> >> Anirban >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy due to Hydrogen bonds
Hi ALL, Is there any means to calculate the total energy arising due to the breaking and formation for hydrogen bonds only in GROMACS? Does the .edr file contains this information? If yes then how to parse it? I don't think the .log file records this value. Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Which .tpr file to use for g_rms?
Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 1 -pbc nojump So which .tpr file should I use? Thanks, Anirban On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham wrote: > On 4/12/2010 4:33 PM, Anirban Ghosh wrote: > >> Thanks a lot for the reply. >> Actually I am running a protein in lipid bilayer. Now I want to >> calculate the thickness of the bilayer at the end of the simulation. >> So for that I want the last structure (.gro) file. So I am trying to >> dump the last structure using trjconv (with -pbc option). So to do >> this which .tpr file should I supply to trjconv, the first one or the >> last one? >> > > Since you're not using the coordinates in the .tpr file to extract the last > frame and map its coordinates onto the .tpr's atom names, it can't matter > what they are. > > Mark > > > Thanks again. >> >> Anirban >> >> On 12/4/10, Justin A. Lemkul wrote: >> >>> >>> Anirban Ghosh wrote: >>> >>>> Thanks a lot Justin for the reply. Yes, I understand that. But ideally >>>> which structure should be used as the reference, in a general, the >>>> starting structure or the end structure? >>>> >>> That's up to you to decide based on what you need to measure. Do you >>> want >>> the >>> RMSD relative to your starting (i.e. crystal/NMR) structure, or are you >>> trying >>> to study how a protein folds, in which case you'd use the native (end) >>> state? >>> >>> like when I an using trjconv to dump my last frame (with "-pbc nojump"), >>>> which .tpr file should I use to get the exact picture of what has >>>> happened to my protein at the end of the simulation. Should I use the >>>> first .tpr file or the last .tpr file? >>>> >>>> I don't understand what you mean. "What has happened" is an entire >>> trajectory, >>> not a snapshot. >>> >>> -Justin >>> >>> Thanks a lot again. >>>> >>>> Anirban >>>> >>>> On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul>>> <mailto:jalem...@vt.edu>> wrote: >>>> >>>> >>>> >>>> Anirban Ghosh wrote: >>>> >>>> Hi ALL, >>>> >>>> Its a very basic question but still... >>>> When we calculate RMSD (or any other parameter) using the g_rms >>>> command, we need to supply the .tpr file with -s option. Now >>>> suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 >>>> ns in each run), then there will be 4 .tpr files. So at the end >>>> of 20 ns if I wish to calculate RMSD, then which .tpr file >>>> should I suppy to g_rms, the first one or the last one? We I run >>>> g_rms with the two .tpr files, I get different results. So which >>>> one should be used? Any suggestion is welcome. >>>> >>>> >>>> Use the one that contains the structure you wish to serve as your >>>> reference. >>>> >>>> -Justin >>>> >>>> >>>> Thanks, >>>> >>>> Anirban >>>> >>>> >>>> -- >>>> >>>> >>>> Justin A. Lemkul >>>> Ph.D. Candidate >>>> ICTAS Doctoral Scholar >>>> MILES-IGERT Trainee >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>> >>>> >>>> -- >>>> gmx-users mailing listgmx-users@gromacs.org >>>> <mailto:gmx-users@gromacs.org> >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>>
Re: [gmx-users] Which .tpr file to use for g_rms?
Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one? Thanks again. Anirban On 12/4/10, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: >> Thanks a lot Justin for the reply. Yes, I understand that. But ideally >> which structure should be used as the reference, in a general, the >> starting structure or the end structure? > > That's up to you to decide based on what you need to measure. Do you want > the > RMSD relative to your starting (i.e. crystal/NMR) structure, or are you > trying > to study how a protein folds, in which case you'd use the native (end) > state? > >> like when I an using trjconv to dump my last frame (with "-pbc nojump"), >> which .tpr file should I use to get the exact picture of what has >> happened to my protein at the end of the simulation. Should I use the >> first .tpr file or the last .tpr file? >> > > I don't understand what you mean. "What has happened" is an entire > trajectory, > not a snapshot. > > -Justin > >> Thanks a lot again. >> >> Anirban >> >> On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul > <mailto:jalem...@vt.edu>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Hi ALL, >> >> Its a very basic question but still... >> When we calculate RMSD (or any other parameter) using the g_rms >> command, we need to supply the .tpr file with -s option. Now >> suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 >> ns in each run), then there will be 4 .tpr files. So at the end >> of 20 ns if I wish to calculate RMSD, then which .tpr file >> should I suppy to g_rms, the first one or the last one? We I run >> g_rms with the two .tpr files, I get different results. So which >> one should be used? Any suggestion is welcome. >> >> >> Use the one that contains the structure you wish to serve as your >> reference. >> >> -Justin >> >> >> Thanks, >> >> Anirban >> >> >> -- >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Which .tpr file to use for g_rms?
Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? like when I an using trjconv to dump my last frame (with "-pbc nojump"), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file? Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Hi ALL, >> >> Its a very basic question but still... >> When we calculate RMSD (or any other parameter) using the g_rms command, >> we need to supply the .tpr file with -s option. Now suppose if I have a >> total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will >> be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then >> which .tpr file should I suppy to g_rms, the first one or the last one? We I >> run g_rms with the two .tpr files, I get different results. So which one >> should be used? Any suggestion is welcome. >> >> > Use the one that contains the structure you wish to serve as your > reference. > > -Justin > > >> Thanks, >> >> Anirban >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Which .tpr file to use for g_rms?
Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Free Energy Calculation: dVpot/dlambda is always zero
Hello Justin, Thanks a lot for the reply. Yes, I am using GROAMCS 4.5 and my system consists of two chains of two proteins, a substrate and an inhibitor solvated in water. So can you please tell me what should be the values for: couple-moltypecouple-lambda0couple-intramolThanks a lot again. Regards, Anirban On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> >> Hi ALL, >> >> I am trying to run free energy calculation and for that in the md.mdp file >> I am keeping the following option: >> >> ; Free energy control stuff >> free_energy = yes >> init_lambda = 0.0 >> delta_lambda= 0 >> sc_alpha=0.5 >> sc-power=1.0 >> sc-sigma= 0.3 >> >> >> But still I find that in my log file the values for dVpot/dlambda is >> always coming to be zero. >> What I am doing wrong? >> Any suggestion is welcome. Thanks a lot in advance. >> >> > You haven't indicated your Gromacs version, but assuming you're using > something in the 4.x series, you're not specifying the necessary parameters > to do any sort of transformation, particularly couple_lambda0 and > couple_lambda1. If left at their default values (vdw-q), nothing gets > decoupled. > > -Justin > > >> Regards, >> >> Anirban >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Free Energy Calculation: dVpot/dlambda is always zero
Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Free Energy Calculation: dVpot/dlambda is always zero
Hi ALL, I am trying to run free energy calculation and for that in the md.mdp file I am keeping the following option: ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda= 0 sc_alpha=0.5 sc-power=1.0 sc-sigma= 0.3 But still I find that in my log file the values for dVpot/dlambda is always coming to be zero. What I am doing wrong? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] WHAM
Hi Justin, Thanks a lot for the reply. Yes I have had a look at section 4.4.2. But section 5.3 tells that this WHAM can be used with the REMD data set as well. So my question is that how to present this REMD data of multiple trajectories as input to WHAM? Do I need to work around with the WHAM code or there is some other way? Any suggestion is welcome. Thanks again. Regards, Anirban On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul wrote: > > > Anirban Ghosh wrote: > >> Hi ALL, >> >> I have carried out REMD simulation on a protein (20 replicas). Now I want >> to carry 2D PMF calculation using RMSD and Radius of gyration as the >> reaction coordinates using Grossfield Lab's WHAM package. For this what >> should be my input parameters to the WHAM program and in which format? >> Any suggestion in this regard is welcome. >> > > I would suggest you consult the documentation for the program (i.e. the > Grossfield WHAM manual, section 4.2.2). I don't know how you intend to pass > your data to a program that is designed for umbrella sampling, but I suppose > that's your task. > > -Justin > > >> >> Regards, >> >> >> Anirban >> >> > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] WHAM
Hi ALL, I have carried out REMD simulation on a protein (20 replicas). Now I want to carry 2D PMF calculation using RMSD and Radius of gyration as the reaction coordinates using Grossfield Lab's WHAM package. For this what should be my input parameters to the WHAM program and in which format? Any suggestion in this regard is welcome. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Bioinformatics Symposium at C-DAC, Pune
The Bioinformatics Group at C-DAC, Pune is going to organize a Symposium on "Accelerating Biology" from December 14-16 2010 at VITS, Pune. You can register for the same at: http://pune.cdac.in/html/events/bioinfo/accelerating_biology/index.aspx Regards, -- Anirban Ghosh C-DAC, Pune, India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd" option with mdrun, right? And why does this curvature of the membrane occurs? Thanks a lot once again. Regards, Anirban On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole wrote: > > Although a bit worrying the curvature of your bilayer is not > responsible for the error message you are seeing. > > to solve the problem you have to increase to use the -rrd option > (see manual for explanation). Typicaly a value of 1.4 to 1.6 should > be fine. > > > On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote: > > Hi ALL, >> >> I have made a CGMD system with multiple copies of a single protein in >> bilayer, by replicating the monomer using genconf in the X-Y plane. After >> running CGMD for about 100 ns, I am getting the following error: >> >> >> >> Energies (kJ/mol) >> Bond G96AngleProper Dih. Improper Dih.LJ (SR) >>4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 >> Coulomb (SR) PotentialKinetic En. Total EnergyTemperature >> -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+053.21675e+02 >> Pressure (bar) Cons. rmsd () >> -9.97540e+001.69233e-05 >> >> >> Not all bonded interactions have been properly assigned to the domain >> decomposition cells >> >> A list of missing interactions: >>G96Angle of 28064 missing 1 >> >> Molecule type 'DSPC' >> the first 10 missing interactions, except for exclusions: >>G96Angle atoms 10 11 12 global 5309 5310 5311 >> >> --- >> Program mdrun_mpi, VERSION 4.0.7 >> Source code file: domdec_top.c, line: 341 >> >> Fatal error: >> 1 of the 62352 bonded interactions could not be calculated because some >> atoms involved moved further apart than the multi-body cut-off distance (1.2 >> nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs >> and tabulated bonds also see option -ddcheck >> >> >> >> On visual inspection I found that the bilayer is becoming curved (image >> attached). In the .top file I have mentioned the different monomers of my >> system as: >> >> >> -- >> [ system ] >> PROT in DSPC Bilayer >> >> [ molecules ] >> Protein 1 >> DSPC 104 >> W 1397 >> NA+ 0 >> CL- 4 >> Protein 1 >> DSPC104 >> W 1397 >> NA+0 >> CL- 4 >> >> - >> >> How can I resolve this error? Any suggestion is welcome. >> >> Regards, >> >> Anirban >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error: Energies (kJ/mol) Bond G96AngleProper Dih. Improper Dih.LJ (SR) 4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 Coulomb (SR) PotentialKinetic En. Total EnergyTemperature -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+053.21675e+02 Pressure (bar) Cons. rmsd () -9.97540e+001.69233e-05 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 28064 missing 1 Molecule type 'DSPC' the first 10 missing interactions, except for exclusions: G96Angle atoms 10 11 12 global 5309 5310 5311 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as: -- [ system ] PROT in DSPC Bilayer [ molecules ] Protein 1 DSPC104 W 1397 NA+ 0 CL- 4 Protein 1 DSPC104 W 1397 NA+0 CL- 4 - How can I resolve this error? Any suggestion is welcome. Regards, Anirban <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Centre of mass removal in CGMD
Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR using CGMD (like you did for rhodopsin), should he/she use the same parameters for COM motion removal? Regards, Anirban On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole wrote: > > On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote: > > Hi ALL, >> >> I am trying to simulate a protein inserted in a lipid bilayer with water >> and ions, the entire system built using CG (coarse grain). I am using the >> Martini force field to the CGMD simulation. My question is that should I use >> the "centre of mass removal" component in my .mdp file (which we do for an >> all-atom protein + lipid simulation)? Should I use the below given >> parameters in my mdp file for this CGMD simulation: >> >> >> - >> ; COM motion removal >> ; These options remove motion of the protein/bilayer relative to the >> solvent/ions >> nstcomm = 1 >> comm-mode = Linear >> comm-grps = Protein_DSPC W >> >> --------- >> > This is the way to go :)) > >> >> Any suggestion is welcome. Thanks a lot in advance. >> >> >> Regards, >> >> Anirban >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Centre of mass removal in CGMD
Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the "centre of mass removal" component in my .mdp file (which we do for an all-atom protein + lipid simulation)? Should I use the below given parameters in my mdp file for this CGMD simulation: - ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W - Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_lie query
Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there any other way (like MMGBSA in Amber) to calculate the free energy for my simulation? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
