[gmx-users] InflateGro methodology
Dear users, I wanna pack the lipids around my protein. To do so, InflateGro methodology is applied. Following Justin's tutorial KALP15-DPPC, the first step is scaling up 4 times: # perl inflategro.pl system.gro 4 POPC 14 system-inflated.gro 5 area.dat and then shrinking it for 26 times. I'd like to know if it is possible to scale up 6 times or more and then scale it down for around 30 times? Because when I scale up 4 times, I see 2,3 lipid chains are still in contact with the protein (I am not sure if this would be a major problem or not!) . Would you please advise me? Thanks 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
Re: [gmx-users] InflateGro methodology
Why don't you just try it and see what happens? On 2012-09-23 12:19:20AM -0700, Shima Arasteh wrote: > > > Dear users, > > I wanna pack the lipids around my protein. To do so, InflateGro methodology > is applied. Following Justin's tutorial KALP15-DPPC, the first step is > scaling up 4 times: > # perl inflategro.pl system.gro 4 POPC 14 system-inflated.gro 5 area.dat > and then shrinking it for 26 times. > > I'd like to know if it is possible to scale up 6 times or more and then scale > it down for around 30 times? Because when I scale up 4 times, I see 2,3 lipid > chains are still in contact with the protein (I am not sure if this would be > a major problem or not!) . > > > Would you please advise me? > > Thanks 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 -- == 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
Re: [gmx-users] InflateGro methodology
I don't know! :)) Sincerely, Shima - Original Message - From: Peter C. Lai To: Discussion list for GROMACS users Cc: Sent: Sunday, September 23, 2012 10:52 AM Subject: Re: [gmx-users] InflateGro methodology Why don't you just try it and see what happens? On 2012-09-23 12:19:20AM -0700, Shima Arasteh wrote: > > > Dear users, > > I wanna pack the lipids around my protein. To do so, InflateGro methodology > is applied. Following Justin's tutorial KALP15-DPPC, the first step is > scaling up 4 times: > # perl inflategro.pl system.gro 4 POPC 14 system-inflated.gro 5 area.dat > and then shrinking it for 26 times. > > I'd like to know if it is possible to scale up 6 times or more and then scale > it down for around 30 times? Because when I scale up 4 times, I see 2,3 lipid > chains are still in contact with the protein (I am not sure if this would be > a major problem or not!) . > > > Would you please advise me? > > Thanks in advance. > > Sincerely, > Shima > -- > gmx-users mailing list 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. > * 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 list 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. * 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] About Warning in grompp
Dear Gromacs users i am doing NPT Eqlibration for a cyclic peptide When I run grompp I have got Warning as follows WARNING 1 [file 2KDQ3.top, line 1137]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H has an estimated oscillational period of 1.0e-02 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. How to Rectify this Warning? If i Neglect using -maxwarn 1 option then have got Segmentation Fault during mdrun Thanks 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
Re: [gmx-users] i have not atomtype K in my input files,
On 9/23/12 1:31 AM, Ali Alizadeh wrote: Dear All users When run grompp program for my system, I encounter this error: grompp -f grompp.mdp -c hyd1.gro -p hyd.top -o hyd.tpr Fatal error: Atomtype K not found But i have not atomtype K in my input files, Apparently you do. Check more closely, especially within any file that is #included. -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 -- 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 Warning in grompp
On 9/23/12 4:17 AM, vidhya sankar wrote: Dear Gromacs users i am doing NPT Eqlibration for a cyclic peptide When I run grompp I have got Warning as follows WARNING 1 [file 2KDQ3.top, line 1137]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H has an estimated oscillational period of 1.0e-02 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. How to Rectify this Warning? The output suggests one way (use of constraints). Otherwise shorten dt if you don't want to use constraints. If i Neglect using -maxwarn 1 option then have got Segmentation Fault during mdrun Overriding warnings is generally a bad idea. grompp is telling you that you have a physically unstable model, so the fact that mdrun crashed is unsurprising. -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 -- 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] pca-based MD
I presume you are referring to Essential Dynamics Sampling, described in section 3.14 of the manual (v4.5.4). There is also a great tool that finds the few PCs that are maximally correlated to a functional quantity (e.g. the volume of the active site). The technique is coined Functional Mode Analysis (FMA) and you can find more information at: http://xray.bmc.uu.se/~jochen/fma.html I have used FMA and worked pretty well in my case. I am wondering if anyone thought of using that technique to find the PCs that are maximally correlated to a functional quantity and then perform Essential Dynamics sampling on these PCs to explore the conformational space that affects the most that functional quantity. I.e. I am studying a kinase in the wt and mutant form. Although the mutation is not near the active site there is a lot of discussion in the literature about the effect of the mutation on the opening of the catalytic cleft. Some people claim that one possible explanation of the over-activity of the mutant is the greater opening of the active site, which facilitates substrate binding and thus leads to enhanced reaction turn-over. In order to test this hypothesis with unbiased MD one would need tremendous computer resources and a lot of time (the kinase is gigantic). On the other hand one could run short simulations of the wt and mutant, do FMA to find the 10-20 PCs that are maximally correlated to the volume of the active site, and then perform Essential Dynamics Sampling on these PCs to explore the conformational space that is highly correlated to the volume of the active site. After that, one could safely claim that the Hypothesis was true or false. I would be interested to read your comments on this. Thomas On 23 September 2012 11:19, James Starlight wrote: > Dear Gromacs Users! > > > There are many publications about implementation of the pca-based MD > simulations for the investigation of the functional-relevant motions. > In that cases the eigenvectors are extracted from the relatively short > MD simulation of the investigated protein and than the biassed MD > simulation is started along chosen principal component which used as > the reaction coordinate. > > I'd like to know more about implementation of that technique in > Gromacs. E.g if I've performed some PCA and extracted eigenvectors how > I can run further simulation along one of the chosen PC ? > > Thanks for help > James > -- > 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 > -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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: Possible bug in the temperature calculation from rerun
On 21/09/2012 11:08 PM, Bastien Loubet wrote: Justin Lemkul wrote On 9/21/12 8:29 AM, Bastien Loubet wrote: Dear gmx users, We recently got a problem with the rerun feature of mdrun, and we request your help in order to help to solve it. We have run a simulation of a large POPC membrane using the coarse grained Martini force fields. From these simulations we obtained a trr trajectory file which contains both the position and the velocity of each martini particle every 20 ps. From this trajectory we rerun the simulation using the -rerun option of the mdrun program but with a different topology for which we have set all the bonded and non bonded interaction to zero. Specifically we have set all the force constant to zero in the martini_v2.P.itp and the martini_v2.0_lipids.itp file, the aim is to calculate the virial due to the electrostatic forces alone. The problem is the following: from the edr file we get from the rerun we extract the mean value of the energies using g_energy. For the edr file obtained during the simulation (and not the rerun) we obtained for the temperature and the kinetic energy, using also a 20ps time interval: Energy Average Err.Est. RMSD Tot-Drift --- Temperature 324.998 0.0049 0.413669 -0.00743801 (K) Kinetic En. 1.9525e+06 292485.21 -44.6815 (kJ/mol) This is to be expected because we have a Nose-Hover temperature coupling of 325 K. The kinetic energy is also equals to the number of degree of freedom times half the Boltzmann constant times the temperature. However for the rerun, with no bonded and non-bonded interactions, we get: Energy Average Err.Est. RMSD Tot-Drift --- Temperature 327.35 0.0053 0.415978 -0.00514402 (K) Kinetic En. 1.96663e+06 322499.08 -30.8973 (kJ/mol) The kinetic energy is again equals to the number of degree of freedom times half the Boltzmann constant times the temperature, however the temperature is 2 K off ! This is surprising as only the velocities and the masses of the particle should enter the kinetic energy. The velocities are taken from the trr trajectory file and we have checked using the Linux diff utility that our topology have the same masses than the original one. Another cause can be that we are doing the rerun on a local machine while the original simulation was run on a cluster, however we believe that this kind of numerical error cannot be responsible for a 2 degree Kelvin mistake. Furthermore we have rerun the simulation using the original topology and we obtained: Energy Average Err.Est. RMSD Tot-Drift --- Temperature 324.998 0.005 0.411827 -0.00761929 (K) Kinetic En. 1.9525e+06 302474.15 -45.7788 (kJ/mol) The slightly different value are certainly due to the previously mentioned fact that the reruns were not run on the same machine as the simulation and numerical rounding errors. This point out that it is really the topology that changes the value of the temperature. However we really have no masses differences between the two topologies and the velocities are draw from the same trr trajectory file. Any thought on this problem would be welcome. Another thing to consider is the fact that an .edr file is accurate over all simulation steps, while reruns only do calculations present in the frames supplied. If you are using frames every 20 ps, that may only represent less than 1% of the total data collected in the simulation, depending on the value of dt. -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 -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Alright, but we did make a rerun with the same trajectory and the original topology and it gives the third results in my original post: the 2 Kelvin difference is not there. So it is really the different topology file that give the temperature difference I believe. The .log file (and grompp) report the number of degrees of freedom per T-coupling group. Search for nrdf in the .log file. Does that differ? What differences are reported for a single trajectory frame? Mark -- g
Re: [gmx-users] pca-based MD
Thomas, thank you for the explanation 1) Indeed ED sampling was exactly that I need. It's not quite understand for me about correct chose of that parameters for biassing simulation -linfix string Indices of eigenvectors for fixed increment linear sampling -linacc string Indices of eigenvectors for acceptance linear sampling -radfix string Indices of eigenvectors for fixed increment radius expansion -radacc string Indices of eigenvectors for acceptance radius expansion -radcon string Indices of eigenvectors for acceptance radius contraction What exactly I need is the biasing of the new MD run along one specified eigenvector which I've extracted from previous run. So it's not quite understand for me what chose would be most correct e.g linnear sampling along that eigenvector or rafius expansion. 2) Also I want to perform such biassing along PC mode extracted from the X-ray data-set of my protein. E.g on first step I calculate PC from the X-ray data-set consisted of different functional relevant conformations of my protein ( for this purpose I need create trajectory from that x-ray data-set firstly). Than I'm looking for one PC which correspond to biological relevant motion ( e.g opening of active center seen in first PC). Finally I want to perform MD from one start structure ( e,g its closed form) along extracted 1 PC from x-ray data-set. For that step I also must make *.edi file for further md_run of the protein firslty. Does this workflow correct in general ? :) 3) This FMA technique is very intresting indeed. As I've understood It can be usefull in case where I could not find biological-relevent motion along one specified PCs ( In that case the combination of the PCs might represent this motion which can correspond to one eigenvector made by FMA). Does it correct ? Thanks again for help, James 2012/9/23 Thomas Evangelidis : > I presume you are referring to Essential Dynamics Sampling, described in > section 3.14 of the manual (v4.5.4). There is also a great tool that finds > the few PCs that are maximally correlated to a functional quantity (e.g. > the volume of the active site). The technique is coined Functional Mode > Analysis (FMA) and you can find more information at: > > http://xray.bmc.uu.se/~jochen/fma.html > > I have used FMA and worked pretty well in my case. I am wondering if anyone > thought of using that technique to find the PCs that are maximally > correlated to a functional quantity and then perform Essential Dynamics > sampling on these PCs to explore the conformational space that affects the > most that functional quantity. > > I.e. I am studying a kinase in the wt and mutant form. Although the > mutation is not near the active site there is a lot of discussion in the > literature about the effect of the mutation on the opening of the catalytic > cleft. Some people claim that one possible explanation of the over-activity > of the mutant is the greater opening of the active site, which facilitates > substrate binding and thus leads to enhanced reaction turn-over. In order > to test this hypothesis with unbiased MD one would need tremendous computer > resources and a lot of time (the kinase is gigantic). On the other hand one > could run short simulations of the wt and mutant, do FMA to find the 10-20 > PCs that are maximally correlated to the volume of the active site, and > then perform Essential Dynamics Sampling on these PCs to explore the > conformational space that is highly correlated to the volume of the active > site. After that, one could safely claim that the Hypothesis was true or > false. > > I would be interested to read your comments on this. > > Thomas > > > On 23 September 2012 11:19, James Starlight wrote: > >> Dear Gromacs Users! >> >> >> There are many publications about implementation of the pca-based MD >> simulations for the investigation of the functional-relevant motions. >> In that cases the eigenvectors are extracted from the relatively short >> MD simulation of the investigated protein and than the biassed MD >> simulation is started along chosen principal component which used as >> the reaction coordinate. >> >> I'd like to know more about implementation of that technique in >> Gromacs. E.g if I've performed some PCA and extracted eigenvectors how >> I can run further simulation along one of the chosen PC ? >> >> Thanks for help >> James >> -- >> 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] pca-based MD
On 23 September 2012 17:18, James Starlight wrote: > Thomas, > > thank you for the explanation > > 1) Indeed ED sampling was exactly that I need. It's not quite > understand for me about correct chose of that parameters for biassing > simulation > > -linfix string Indices of eigenvectors for fixed increment > linear sampling > -linacc string Indices of eigenvectors for acceptance linear > sampling > -radfix string Indices of eigenvectors for fixed increment > radius expansion > -radacc string Indices of eigenvectors for acceptance radius > expansion > -radcon string Indices of eigenvectors for acceptance radius > contraction > > What exactly I need is the biasing of the new MD run along one > specified eigenvector which I've extracted from previous run. So it's > not quite understand for me what chose would be most correct e.g > linnear sampling along that eigenvector or rafius expansion. > > Unfortunately I haven't ever used ED sampling myself so someone else might explain what these parameters are meant for. > 2) Also I want to perform such biassing along PC mode extracted from > the X-ray data-set of my protein. E.g on first step I calculate PC > from the X-ray data-set consisted of different functional relevant > conformations of my protein ( for this purpose I need create > trajectory from that x-ray data-set firstly). Than I'm looking for one > PC which correspond to biological relevant motion ( e.g opening of > active center seen in first PC). Finally I want to perform MD from one > start structure ( e,g its closed form) along extracted 1 PC from x-ray > data-set. For that step I also must make *.edi file for further md_run > of the protein firslty. Does this workflow correct in general ? :) > > > 3) This FMA technique is very intresting indeed. As I've understood It > can be usefull in case where I could not find biological-relevent > motion along one specified PCs ( In that case the combination of the > PCs might represent this motion which can correspond to one > eigenvector made by FMA). Does it correct ? > It is highly unlikely that a functionally relevant motion is explained by a single PC. FMA gives the degree in which each PC affects (and thus is correlated to) the functional quantity you chose (e.g. the volume of the active site), it does not give you a single eigenvector. For instance you may have found that the opening of your active site is well explained by the first PC. Yet, FMA may give you that this functional quantity (volume of the active site) is affected from the 1st PC by 70%, from the 2nd by 5%, from the 3rd by 12%, and from the 4th by 7% and to the 5th by 6%. It is more accurate then to use PC1-5 in ED sampling. > 2012/9/23 Thomas Evangelidis : > > I presume you are referring to Essential Dynamics Sampling, described in > > section 3.14 of the manual (v4.5.4). There is also a great tool that > finds > > the few PCs that are maximally correlated to a functional quantity (e.g. > > the volume of the active site). The technique is coined Functional Mode > > Analysis (FMA) and you can find more information at: > > > > http://xray.bmc.uu.se/~jochen/fma.html > > > > I have used FMA and worked pretty well in my case. I am wondering if > anyone > > thought of using that technique to find the PCs that are maximally > > correlated to a functional quantity and then perform Essential Dynamics > > sampling on these PCs to explore the conformational space that affects > the > > most that functional quantity. > > > > I.e. I am studying a kinase in the wt and mutant form. Although the > > mutation is not near the active site there is a lot of discussion in the > > literature about the effect of the mutation on the opening of the > catalytic > > cleft. Some people claim that one possible explanation of the > over-activity > > of the mutant is the greater opening of the active site, which > facilitates > > substrate binding and thus leads to enhanced reaction turn-over. In order > > to test this hypothesis with unbiased MD one would need tremendous > computer > > resources and a lot of time (the kinase is gigantic). On the other hand > one > > could run short simulations of the wt and mutant, do FMA to find the > 10-20 > > PCs that are maximally correlated to the volume of the active site, and > > then perform Essential Dynamics Sampling on these PCs to explore the > > conformational space that is highly correlated to the volume of the > active > > site. After that, one could safely claim that the Hypothesis was true or > > false. > > > > I would be interested to read your comments on this. > > > > Thomas > > > > > > On 23 September 2012 11:19, James Starlight > wrote: > > > >> Dear Gromacs Users! > >> > >> > >> There are many publications about implementation of the pca-based MD > >
Re: [gmx-users] pca-based MD
Thomas, thanks again for explanation. Its also intresting to me is it possible to do further biassed MD guided on that FMA modes as well as obtain projections onto that FMA sub-spaces of X-ray datasets for instance ? ( e.g for comparison of the results from FMA of experimental data as well as MD_data) James 2012/9/23 Thomas Evangelidis : > On 23 September 2012 17:18, James Starlight wrote: > >> Thomas, >> >> thank you for the explanation >> >> 1) Indeed ED sampling was exactly that I need. It's not quite >> understand for me about correct chose of that parameters for biassing >> simulation >> >> -linfix string Indices of eigenvectors for fixed increment >> linear sampling >> -linacc string Indices of eigenvectors for acceptance linear >> sampling >> -radfix string Indices of eigenvectors for fixed increment >> radius expansion >> -radacc string Indices of eigenvectors for acceptance radius >> expansion >> -radcon string Indices of eigenvectors for acceptance radius >> contraction >> >> What exactly I need is the biasing of the new MD run along one >> specified eigenvector which I've extracted from previous run. So it's >> not quite understand for me what chose would be most correct e.g >> linnear sampling along that eigenvector or rafius expansion. >> >> > Unfortunately I haven't ever used ED sampling myself so someone else might > explain what these parameters are meant for. > > > >> 2) Also I want to perform such biassing along PC mode extracted from >> the X-ray data-set of my protein. E.g on first step I calculate PC >> from the X-ray data-set consisted of different functional relevant >> conformations of my protein ( for this purpose I need create >> trajectory from that x-ray data-set firstly). Than I'm looking for one >> PC which correspond to biological relevant motion ( e.g opening of >> active center seen in first PC). Finally I want to perform MD from one >> start structure ( e,g its closed form) along extracted 1 PC from x-ray >> data-set. For that step I also must make *.edi file for further md_run >> of the protein firslty. Does this workflow correct in general ? :) >> >> >> 3) This FMA technique is very intresting indeed. As I've understood It >> can be usefull in case where I could not find biological-relevent >> motion along one specified PCs ( In that case the combination of the >> PCs might represent this motion which can correspond to one >> eigenvector made by FMA). Does it correct ? >> > > It is highly unlikely that a functionally relevant motion is explained by a > single PC. FMA gives the degree in which each PC affects (and thus is > correlated to) the functional quantity you chose (e.g. the volume of the > active site), it does not give you a single eigenvector. For instance you > may have found that the opening of your active site is well explained by > the first PC. Yet, FMA may give you that this functional quantity (volume > of the active site) is affected from the 1st PC by 70%, from the 2nd by 5%, > from the 3rd by 12%, and from the 4th by 7% and to the 5th by 6%. It is > more accurate then to use PC1-5 in ED sampling. > > > >> 2012/9/23 Thomas Evangelidis : >> > I presume you are referring to Essential Dynamics Sampling, described in >> > section 3.14 of the manual (v4.5.4). There is also a great tool that >> finds >> > the few PCs that are maximally correlated to a functional quantity (e.g. >> > the volume of the active site). The technique is coined Functional Mode >> > Analysis (FMA) and you can find more information at: >> > >> > http://xray.bmc.uu.se/~jochen/fma.html >> > >> > I have used FMA and worked pretty well in my case. I am wondering if >> anyone >> > thought of using that technique to find the PCs that are maximally >> > correlated to a functional quantity and then perform Essential Dynamics >> > sampling on these PCs to explore the conformational space that affects >> the >> > most that functional quantity. >> > >> > I.e. I am studying a kinase in the wt and mutant form. Although the >> > mutation is not near the active site there is a lot of discussion in the >> > literature about the effect of the mutation on the opening of the >> catalytic >> > cleft. Some people claim that one possible explanation of the >> over-activity >> > of the mutant is the greater opening of the active site, which >> facilitates >> > substrate binding and thus leads to enhanced reaction turn-over. In order >> > to test this hypothesis with unbiased MD one would need tremendous >> computer >> > resources and a lot of time (the kinase is gigantic). On the other hand >> one >> > could run short simulations of the wt and mutant, do FMA to find the >> 10-20 >> > PCs that are maximally correlated to the volume of the active site, and >> > then perform Essential Dynamics Sampling o
Re: [gmx-users] force field parameters
Please keep the discussion on the list. On 9/23/12 11:45 AM, Asaf Farhi wrote: Dear Justin Thank you very much for the reply. I apologize that I take of your time. I need this file in order to demonstrate a method for free energy calculation that I'm working on (using Matlab). I don't have Gromacs installed. If you can, and it's legal I would be happy to have such a file so I can use realistic parameters in the simulation. I haven't found such a list with units and I've spent almost a day in total. I will cite the relevant article of course. Gromacs is free to download. Obtain the source from www.gromacs.org. You don't even need to install it to access any of the files you need. They are all in the /share/top/*.ff subdirectories of the source tree. -Justin Thanks again, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Saturday, September 22, 2012 10:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force field parameters On 9/22/12 2:13 PM, Asaf Farhi wrote: Dear Justin Thank you very much for the reply. Can you please instruct me how to download the file? Each force field has an ffbonded.itp when Gromacs is installed. They are located in $GMXLIB/whatever.ff/ -Justin Thanks, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Saturday, September 22, 2012 3:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force field parameters On 9/22/12 8:48 AM, Asaf Farhi wrote: Dear Users Hi. I'm looking for a a list of bond stretching parameters for the potential 0.5k(r-r_eq)^2 that has units (k and r_eq). Can anyone help me with that (article will be good)? All of that information is in the ffbonded.itp file for whatever force field you like. Citations for all of them are in the manual. -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 -- 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 -- 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 -- 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 -- 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 -- 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
FW: [gmx-users] force field parameters
Dear Justin Thank you very much for the reply. I apologize that I take of your time. I need this file in order to demonstrate a method for free energy calculation (using Matlab). I don't have Gromacs installed. If you can, and it's legal I would be happy to have such a file so I can use realistic parameters in the simulation. I haven't found such a list with units and I've spent almost a day in total. I will cite the relevant article of course. Thanks again, Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Saturday, September 22, 2012 10:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force field parameters On 9/22/12 2:13 PM, Asaf Farhi wrote: > Dear Justin > > Thank you very much for the reply. > Can you please instruct me how to download the file? > Each force field has an ffbonded.itp when Gromacs is installed. They are located in $GMXLIB/whatever.ff/ -Justin > Thanks, > Best regards, > Asaf > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin Lemkul [jalem...@vt.edu] > Sent: Saturday, September 22, 2012 3:53 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] force field parameters > > On 9/22/12 8:48 AM, Asaf Farhi wrote: >> Dear Users >> >> Hi. I'm looking for a a list of bond stretching parameters for the potential >> 0.5k(r-r_eq)^2 that has units (k and r_eq). >> Can anyone help me with that (article will be good)? >> > > All of that information is in the ffbonded.itp file for whatever force field > you > like. Citations for all of them are in the manual. > > -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 > > > -- > 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 > -- 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 -- 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] PCA comparison between two simulations
Hi, I would first do an alignment between the two proteins and then do PCA using only the Ca atom coordinates of the common atoms (or the ones you think are equivalent). I would also remove the very flexible loops to extract pure low-frequency motions with PCA. At the end you must have two eigenspaces that correspond to the same number of Ca atoms, which you can compare using the Root Mean Square Inner Product of selected PCs. For example, to measure the inner productions between eigenvectors 1-3 you can use: g_anaeig -v eigenvec1.trr -eig eigenval1.xvg -v2 eigenvec2.trr -eig2 eigenval2.xvg -inpr -first 1 -last 3 There are a few more option of g_anaeig you can experiment with. HTH, Thomas On 23 September 2012 18:25, francesco oteri wrote: > Dear gromacs users, > I've simulated two different proteins (different atom number) and I carried > out the pca analysis > for the two simulations. Now I'd like to know whether there is a similarity > between the eigenvectors > of the two simulation, i.e. whether the 1st eigenvector of simulation1 is > similar to the 3rd eigenvector > of simulation2. In my case, the eigenvector direction is enough as > definition of similarity. > > Can you help me? please > > > Francesco > -- > 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 > -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] Analysis of enssemble of MD trajectories
Justin, Francesco, thanks for advises. James 2012/9/21 Justin Lemkul : > > > On 9/21/12 2:11 AM, James Starlight wrote: >> >> Dear collegues >> >> Thank for advices. Indeed Gromacs is able to analyse two trajectories >> with g_rms ( with the flags -f and -f2 ) but as the result I've obtain >> graph with one rmsd plot so I'm not sure about implementation of that >> method. >> >> So I think that the algorithm proposed by Justin was exactly what I >> need. But I'm not sure also how I could do such ploating of results of >> the different g_rms analyses to one common graph ( when I analyse new >> trajectory and save it by the -o result.xvg if the result.xvg was >> already exist the old graph is back up to the #result.xvg# etc ). >> > > Choose new file names each time. If you have, for instance, result1.xvg, > result2.xvg, and result3.xvg, just load them in XmGrace: > > xmgrace result*.xvg & > > They will all appear in the same plotting area. > > > -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 > > > -- > 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] TIP4P water model
Hi, So the commands from the beginning are appended below: pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro (I choose option 6 for AMBER99sb-ILDN force field and then option 2 for TIP4P water model) editconf -f system.gro -o system_box.gro -c -d 1.0 -bt dodecahedron genbox -cp system_box.gro -cs tip4p.gro -o system_solv.gro -p topol.top grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr And it is here that I get the error : Fatal error: number of coordinates in coordinate file (system_solv.gro, 421880) does not match topology (topol.top, 416008) I am appending below the contents of my topology file: ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Fri Sep 21 14:02:35 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx_d - VERSION 4.5.5 ; ; Command line was: ; /usr/local/src/gromacs/bin/pdb2gmx_d -vsite h -f 3HQN_tet-nolig.pdb -o system.gro ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Protein_chain_A2.itp" #include "topol_Protein_chain_B.itp" #include "topol_Protein_chain_B2.itp" #include "topol_Protein_chain_C.itp" #include "topol_Protein_chain_C2.itp" #include "topol_Protein_chain_D.itp" #include "topol_Protein_chain_D2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip4p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A2 1 Protein_chain_B 1 Protein_chain_B2 1 Protein_chain_C 1 Protein_chain_C2 1 Protein_chain_D 1 Protein_chain_D2 1 SOL 340 SOL 394 SOL 340 SOL 394 SOL 94333 --- I cannot understand as to why it is generating error at this stage. It would be really helpful if you could advice me how to proceed from here. Best Wishes, Ankita On Sat, Sep 22, 2012 at 12:57 AM, Justin Lemkul wrote: > > > On 9/21/12 7:55 PM, Peter C. Lai wrote: >> >> Perhaps genion is not removing the dummy atoms properly? >> > > The problem is occurring with grompp before genion. We would need to see > all the prior commands (exactly copied and pasted from the terminal) as well > as the [molecules] section of the topology, to at least start to guess at > what's wrong. It is unusual to find a failure in grompp before genion. > > -Justin > > >> On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote: >>> >>> Hi all, >>> >>> I am trying to begin a simulation of a protein. >>> >>> I am using AMBER99sb-ILDN force field and TIP4P water model. However, >>> I am facing a problem in the ion adding step. >>> >>> when I issue the grompp command to generate the necessary .tpr file >>> for simulation to be utilised by genion tool, I get the following >>> error : >>> >>> "Fatal error: >>> number of coordinates in coordinate file (system_solv.gro, 421880) >>> does not match topology (topol.top, 416008) >>> " >>> >>> However, I have rechecked several times my topology file and the >>> co-ordinate file and I am running it pretty straightforward to get >>> this error. When I try TIP3P water model for the same protein, I do >>> not get the error. >>> >>> I get the same error when I use TIP4P-Ew water model too. I have >>> decide a better water model for my system before I run my final >>> production simulations and so I have been trying to compare both the >>> water models. I am wondering if anyone could kindly suggest the >>> possible reason for this error because ideally, it should not be >>> giving me any error at this stage as I haven't manipulated with >>> anything. >>> >>> I am also appending my ions.mdp info below: >>> >>> ; ions.mdp - used as input into grompp to generate ions.tpr >>> ; Parameters describing what to do, when to stop and what to save >>> integrator = steep ; Algorithm (steep = steepest descent >>> minimization) >>> emtol = 1000.0; Stop minimization when the maximum >>> force < 1000.0 kJ/mol/nm >>> emstep = 0.01 ; Energy step size >>> nsteps = 5 ; Maximum number of (minimization) steps >>> to perform >>> >>> ; Parameters describing how to find the neighbors of each atom and how >>> to calculate the interactions >>> nstlist = 1 ; Frequency to update the neighbor list >>> and long range forces >>> ns_type = grid ; Method to determine neighbor list >>> (simple, grid) >>> rlist = 0.9 ;
Re: [gmx-users] TIP4P water model
On 9/23/12 2:28 PM, Ankita naithani wrote: Hi, So the commands from the beginning are appended below: pdb2gmx -vsite h -f 3HQN_tet_nolig.pdb -o system.gro (I choose option 6 for AMBER99sb-ILDN force field and then option 2 for TIP4P water model) editconf -f system.gro -o system_box.gro -c -d 1.0 -bt dodecahedron genbox -cp system_box.gro -cs tip4p.gro -o system_solv.gro -p topol.top grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr And it is here that I get the error : Fatal error: number of coordinates in coordinate file (system_solv.gro, 421880) does not match topology (topol.top, 416008) I am appending below the contents of my topology file: ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Fri Sep 21 14:02:35 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx_d - VERSION 4.5.5 ; ; Command line was: ; /usr/local/src/gromacs/bin/pdb2gmx_d -vsite h -f 3HQN_tet-nolig.pdb -o system.gro ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Protein_chain_A2.itp" #include "topol_Protein_chain_B.itp" #include "topol_Protein_chain_B2.itp" #include "topol_Protein_chain_C.itp" #include "topol_Protein_chain_C2.itp" #include "topol_Protein_chain_D.itp" #include "topol_Protein_chain_D2.itp" ; Include water topology #include "amber99sb-ildn.ff/tip4p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_A2 1 Protein_chain_B 1 Protein_chain_B2 1 Protein_chain_C 1 Protein_chain_C2 1 Protein_chain_D 1 Protein_chain_D2 1 SOL 340 SOL 394 SOL 340 SOL 394 SOL 94333 --- I cannot understand as to why it is generating error at this stage. It would be really helpful if you could advice me how to proceed from here. The difference in the number of atoms (5872) is exactly equal to 4 * (340 + 394 + 340 + 394), so the presence of multiple SOL entries is causing a problem. Verify that these molecules are indeed in TIP4P form, and if they are (i.e. they were correctly constructed in pdb2gmx), try merging the SOL blocks into one single entry in the topology. -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 -- 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] pca-based MD
Hi, thanks again for explanation. Its also intresting to me is it possible > to do further biassed MD guided on that FMA modes as well as obtain > projections onto that FMA sub-spaces of X-ray datasets for instance ? > ( e.g for comparison of the results from FMA of experimental data as > well as MD_data) > > Have a look at another thread posted today, named "PC comparison between two simulations". On a second thought, you might want to consider the nudged elastic band method and its variants for your case, since you have the initial, the final and intermediate states of your protein. Unfortunately they are not implemented in GROMACS, but they are in AMBER. Thomas -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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] elastic network model - normal mode analysis
On 23/09/2012 5:22 PM, mohan maruthi sena wrote: Hi all, I want to do normal mode analysis for a protein using elastic network model containing 691 residues. I consider only c-alpha atoms connected by a spring constant of 81600 kj/nm2. When I do normal mode analysis I get the following error : Maximum force: 6.30230e+02 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. Finished step 691 out of 691 I have minimised the structure , still i get the same error. I use in gromacs 4.5.5 double precision for these simulations. When I load the trajectory eigen.trr in vmd(to see normal modes) , I could see the protein far away and all atoms overlapped. I use the following .mdp file parameters as input ; RUN CONTROL PARAMETERS integrator = nm dt = 0.002 ; time step (ps) nsteps = 100 ; number of steps ; OUTPUT CONTROL OPTIONS nstenergy= 500 nstxout = 500 nstvout = 500 nstfout = 500 energygrps = System ; NEIGHBORSEARCHING PARAMETERS nstlist = 0 #Frequency to update neighbourlist pbc = no comm_mode = ANGULAR ; OPTIONS FOR ELECTROSTATICS AND VDW ; Temperature coupling tcoupl = v-rescale ; Couple temperature to external heat bath according to Berendsen method tc-grps = System ;Non-Protein ; Use separate heat baths for Protein and Non-Protein groups tau_t= 0.2 ;0.2 ; Coupling time constant, controlling strength of coupling ref_t= 300; Temperature of heat bath ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distribution gen_temp = 300.0 ; Temperature to generate corresponding Maxwell distribution gen_seed = ; Seed for (semi) random number generation. Different numbers give different sets of velocities ; OPTIONS FOR BONDS constraints = none ; No constraints except for those defined explicitly in the topology refcoord_scaling = com Please suggest me a way to rectify this error. You're doing something wrong in the construction of your model. Find a toy example in the literature that you can attempt to copy so that you know you know how to walk before you try to run. Failing that, construct some geometric solid that should be stable, like a tetragonal pyramid, or something. Until you can do that, worrying about a protein is a waste of time. The strength of your forces, temperature and size of your time step are all closely interlinked if you want the integration to do something sensible, and probably you're inventing all of them at the moment. Mark -- 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] Missing charges in a .gro file
Dear all, I have created a .GRO file from a PDB file for a polymer. However in the PDB I have positive and negative charges of some ions where as in the produced GRO file these disappear. Are those charged atoms taken into account in the gro file as I will be doing a MD simulation of such polymers with nanotubes later and I dont want to work with the wrong GRO fileif the answer is no, how do I include them? Thanks Regards ELie -- 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] Missing charges in a .gro file
On Mon, Sep 24, 2012 at 12:56 PM, Elie M wrote: > > Dear all, > I have created a .GRO file from a PDB file for a polymer. However in the > PDB I have positive and negative charges of some ions where as in the > produced GRO file these disappear. Are those charged atoms taken into > account in the gro file as I will be doing a MD simulation of such polymers > with nanotubes later and I dont want to work with the wrong GRO fileif > the answer is no, how do I include them? Thanks > Regards > ELie -- > http://manual.gromacs.org/online/gro.html http://manual.gromacs.org/online/top.html There are no charges in .gro files. The charges are probably discarded in your way. Terry 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] Missing charges in a .gro file
Thanks for your help. Elie > Date: Mon, 24 Sep 2012 13:05:14 +0800 > Subject: Re: [gmx-users] Missing charges in a .gro file > From: terrence...@gmail.com > To: gmx-users@gromacs.org > > On Mon, Sep 24, 2012 at 12:56 PM, Elie M wrote: > > > > > Dear all, > > I have created a .GRO file from a PDB file for a polymer. However in the > > PDB I have positive and negative charges of some ions where as in the > > produced GRO file these disappear. Are those charged atoms taken into > > account in the gro file as I will be doing a MD simulation of such polymers > > with nanotubes later and I dont want to work with the wrong GRO fileif > > the answer is no, how do I include them? Thanks > > Regards > > ELie -- > > > > http://manual.gromacs.org/online/gro.html > http://manual.gromacs.org/online/top.html > There are no charges in .gro files. The charges are probably discarded in > your way. > > Terry > > > 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] pca-based MD
I've tried to make PCA from my X-ray data and forced with many problems :) Firstly I've made pdb trajectory in NMR-like format ( by means of pymol) consisted of all X-ray structures. than I've make .tpr file (From the tpr of the same protein which I've simulated previously) for the subset of C-alpha atoms common to all structures Finally I've tried to calculate eigenvectors Structure or trajectory file has more atoms (2196) than the topology (302) Does it mean that all structures in trajectory must have only C-alpha atoms initialy ? IS there another way to make tpr as well as pdb trajectory files for such x-ray PCA? James 2012/9/24 Thomas Evangelidis : > Hi, > > thanks again for explanation. Its also intresting to me is it possible >> to do further biassed MD guided on that FMA modes as well as obtain >> projections onto that FMA sub-spaces of X-ray datasets for instance ? >> ( e.g for comparison of the results from FMA of experimental data as >> well as MD_data) >> >> > Have a look at another thread posted today, named "PC comparison between > two simulations". > > On a second thought, you might want to consider the nudged elastic band > method and its variants for your case, since you have the initial, the > final and intermediate states of your protein. Unfortunately they are not > implemented in GROMACS, but they are in AMBER. > > Thomas > > -- > > == > > Thomas Evangelidis > > PhD student > University of Athens > Faculty of Pharmacy > Department of Pharmaceutical Chemistry > Panepistimioupoli-Zografou > 157 71 Athens > GREECE > > email: tev...@pharm.uoa.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > -- > 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] Fast exchanges for REMD
Dear all,
I've done some REMD simulations using a quite high exchange attempt
frequency (10 attempts per ps) as proposed by Sindhikara et al.
("Exchange Often and Properly in Replica Exchange Molecular Dynamics",J.
Chem. Theory Comput. 2010, 6, 2804–2808 ).
Unfortunately, I have now recognized that the demux perl script cannot
account for an EAF which is higher than the saving frequency in the
trajectory.
Comments from demux.pl:
# If your exchange was every N ps and you saved every M ps you can make for
# the missing frames by setting extra to (N/M - 1). If N/M is not integer,
# you're out of luck and you will not be able to demux your trajectories
at all.
In my case exchanges every 0.1 ps and saved every 5 ps
Changing the demux.pl script, so that it writes the "replica_index.xvg"
with a higher precision (time in ps) should be no problem. However, my
question is: will this work together with trjcat? Does trjcat search for
the timeframe given in the first column of "replica_index.xvg", or does
it links each line to one saved timeframe? If so, could I just delete
the additional lines in "replica_index.xvg"?
I would be really happy if someone could help me with this!
Thanks!
Andi
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