Re: [gmx-users] Overlap between PC motions
Hi Tsjerk, I really appreciate your comments. I proceeded as you recommended, and calculate the subspace overlap in the way you proposed. I first performed the analysis varying the starting points, instead of the end ones. I start from 110 ns down to 0ns, with 10ns time intervals: Normalized DT 0.402110-100ns 0.456110-90ns 0.472110-80ns 0.485110-70ns 0.570110-60ns 0.585110-50ns 0.594110-40ns 0.595110-30ns 0.598110-20ns 0.602110-10ns 1.000 Ttot The analysis and visual inspection of the trajectory revealed that the system, made up of six interacting monomers, is very stable. An Hbond is formed at the half of the simulation since the N-terminal moiety of one of these monomers moves towards another monomer. After my wrong conception and based on your comments, now I think that the point is that the system was relaxing towards that conformation and that was the reason of the 1.000 values for the subspace overlap in the first email I posted. I have read through the bibliography that to have an estimation of whether these values are indicative of good convergence is required a comparison with similar systems. However, to understand the meaning of the method I also did the covariance analysis on the last part of the trajectory, first varying the end points (70-75; 70-80; 70-85 ... 70-110) and then varying the starting ones (110-105; 110-100 ... 110-70) and I got the following values: Normalized DT 0.503110-105ns 0.735110-100ns 0.821110-95ns 0.947110-90ns 1.000110-85ns 1.000110-80ns 1.000110-75ns 1.000110-70ns Normalized DT 0.43970-75 ns 0.56470-80 ns 0.61470-85 ns 0.63970-90 ns 0.89570-95 ns 1.00070-100ns 1.00070-105ns 1.00070-110ns I do not know if I am wrong, but the relaxation is observed when varying the end points (0-10, 0-20, 0-30 ... 0-110), and proceeding the reverse way (110-100, 110-90, 110-80 ... 110-0) the results seem to make more sense. However, when performing the covariance analysis on the last part of the trajectory the thing of the covariance matrices being equal before reaching the time window that covers the whole time analyzed is getting me confused. It is expected to get so many 1.000-values? I do not see the point for the covariance matrices being equal when varying the starting points. Regards, Miguel 2013/5/30 Tsjerk Wassenaar > Hi Miguel, > > The fitting doesn't play a role; it's the dynamics of the system in the > internal frame. Because the internal frame moves, you fit, so that any > contribution due to the rigid body motion is removed. > > For the rest you have to look at it like this: You start out somewhere and > walk (relax) towards some city, several kilometers away. You get there and > get lost in the streets, making random walks. Now, what you do with > covariance analysis is looking at the displacements around the mean > position. Your mean position will lie somewhere between your starting > position and the place where you ended up. The deviations from the mean > will be dominated by vectors pointing from wherever you are in the city > towards your starting point. That will be reflected in the covariance > matrix, which doesn't change much, certainly not in terms of the directions > of the first few eigenvectors. > Probably you're actually more interested in the things you do in the city, > your native configuration energy well. But to analyze that, you have to cut > off the part of the journey that brought you there. So it makes sense to do > the covariance analysis on the last half or quarter of the trajectory. It > would also be interesting to check the convergence from the other side of > the trajectory, varying the starting point of the analysis, rather than the > end point. > > > Hope it helps, > > Tsjerk > > > On Thu, May 30, 2013 at 1:37 PM, Miguel Ángel Mompeán García < > mig.momp...@gmail.com> wrote: > > > Hi Tsjerk, > > > > Thanks for the reply! So, let me see if I am getting the things right. > The > > same fitting structure is used for the overlap calculation. Since the > > averaged structure is used for the covariance matrices, this is the > reason > > why the relaxation is included. Am I right? > > The overall behavior of the system is that the structure keeps very > > "compact" and one additional hydrogen bond between two residues is formed > > at ~60ns, and stable till the end of the run, as computed with g_hbond. > > That interaction is already present in the average structure. So if I > > understood properly your comment, from the time window 0-70 up to the > end, > > there will not be significant contributions to the covarianc
Re: [gmx-users] Overlap between PC motions
Hi Tsjerk, Thanks for the reply! So, let me see if I am getting the things right. The same fitting structure is used for the overlap calculation. Since the averaged structure is used for the covariance matrices, this is the reason why the relaxation is included. Am I right? The overall behavior of the system is that the structure keeps very "compact" and one additional hydrogen bond between two residues is formed at ~60ns, and stable till the end of the run, as computed with g_hbond. That interaction is already present in the average structure. So if I understood properly your comment, from the time window 0-70 up to the end, there will not be significant contributions to the covariance matrix. Thanks for your valuable comments. Highly appreciated! 2013/5/30 Tsjerk Wassenaar > Hi Miguel, > > Sorry for not responding earlier, but the question isn't really simple :) > What you do is determining the covariance matrix from the start up to a > certain point and see for different end points what the overlap is with the > covariance matrix from the whole. This means that in all cases, the > relaxation of the system is included, and this is the dominant contribution > to your covariance matrix. At some point, the system has reached the region > around B and then stays there. All kinds of things may be happening, but > they're overwhelmed by the changes associated with the relaxation. Hence, > the part of the trajectory after 70 ns doesn't contribute significantly to > the covariance matrix anymore. > > Hope it helps, > > Tsjerk > > > > On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García < > mig.momp...@gmail.com> wrote: > > > Dear all, > > > > I posted some days ago an issue regarding overlap values. If any of you > is > > experienced with this I would appreciate some comments. Please find below > > the mentioned post: > > > > > > I am doing PCA on a 110ns run. > > When calculating the subspace overlap from independent PCA performed in > > different time windows, I expect the overlap to be 1 only when the time > > interval is equal to 110ns, since both covariance matrices are identical. > > However, I found that from the interval 0-70 forwards (I'm increasing > each > > window in 10ns) the overlap reaches that value. Is this expected? From > the > > rmsd, cosine content and visual inspection of the trajectory I expected > > small changes from this point till the total time, but not the two > matrices > > being equal... Am I doing something wrong or this may happen? > > > > Here is my data set of results: > > > > Normalized Shape DT > > 0.6110.6380-10ns > > 0.6160.6500-20ns > > 0.6460.6710-30ns > > 0.6560.6780-40ns > > 0.6590.6830-50ns > > 0.8730.9190-60ns > > 1.0001.0000-70ns > > 1.0001.0000-80ns > > 1.0001.0000-90ns > > 1.0001.0000-100ns > > 1.0001.0000-110ns = Ttot > > > > > > Regards, > > Miguel > > -- > > 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] Overlap between PC motions
Dear all, I posted some days ago an issue regarding overlap values. If any of you is experienced with this I would appreciate some comments. Please find below the mentioned post: I am doing PCA on a 110ns run. When calculating the subspace overlap from independent PCA performed in different time windows, I expect the overlap to be 1 only when the time interval is equal to 110ns, since both covariance matrices are identical. However, I found that from the interval 0-70 forwards (I'm increasing each window in 10ns) the overlap reaches that value. Is this expected? From the rmsd, cosine content and visual inspection of the trajectory I expected small changes from this point till the total time, but not the two matrices being equal... Am I doing something wrong or this may happen? Here is my data set of results: Normalized Shape DT 0.6110.6380-10ns 0.6160.6500-20ns 0.6460.6710-30ns 0.6560.6780-40ns 0.6590.6830-50ns 0.8730.9190-60ns 1.0001.0000-70ns 1.0001.0000-80ns 1.0001.0000-90ns 1.0001.0000-100ns 1.0001.0000-110ns = Ttot Regards, Miguel -- 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] subspace overlap
Dear all, I am doing PCA on a 110ns run. When calculating the subspace overlap from independent PCA performed in different time windows, I expect the overlap to be 1 only when the time interval is equal to 110ns, since both covariance matrices are identical. However, I found that from the interval 0-70 forwards (I'm increasing each window in 10ns) the overlap reaches that value. Is this expected? From the rmsd, cosine content and visual inspection of the trajectory I expected small changes from this point till the total time, but not the two matrices being equal... Am I doing something wrong or this may happen? Here is my data set of results: Normalized Shape DT 0.6110.6380-10ns 0.6160.6500-20ns 0.6460.6710-30ns 0.6560.6780-40ns 0.6590.6830-50ns 0.8730.9190-60ns 1.0001.0000-70ns 1.0001.0000-80ns 1.0001.0000-90ns 1.0001.0000-100ns 1.0001.0000-110ns = Ttot -- 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] X particles communicated to PME node Y are more ...
2013/3/4 Justin Lemkul > Dear Justin, > With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1 If you find something weird in the mdp file or require further explanations on the points do mention I will do my best to provide the necessary info. Right below are the comments: > In that case, it's probably something worth pursuing. Having the new > version fail when an older version works is curious. Can you please > provide all of the following details: > > 1. Compilers used to build Gromacs > 2. Hardware description These lines are from the CMakeOutput.log file: The system is: Linux - 2.6.32-5-amd64 - x86_64(*) Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded. Compiler: /usr/bin/gcc cc -v: gcc version 4.4.5 3. mdrun command > 4. Complete .mdp file grompp -f minimize.mdp -c Mut3.gro -o em.tpr -p topol.top mdrun -v -deffnm em The minimize.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5 nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 pbc = xyz Thank-you a lot for all your tips and comments, Miguel > > > -Justin > > 2013/3/4, Justin Lemkul : >> >>> >>> >>> On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote: >>> >>>> I have tried the same issue (same system with same mdp file and same >>>> initial configuration as starting structure) and is running without >>>> any problems with GROMACS-4.5.5. >>>> >>>> Anyone knows what is happening? >>>> >>>> >>> You didn't tell us your Gromacs version in the previous post so the best >>> guess >>> is "random bug that was somehow fixed before 4.5.5." >>> >>> -Justin >>> >>> >>>> 2013/3/4, Justin Lemkul : >>>> >>>>> >>>>> >>>>> On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: >>>>> >>>>>> Dear gmx users, >>>>>> >>>>>> I have successfully performed simulations on a charged peptide. I did >>>>>> a >>>>>> series of mutations and everything had a happy end. Now I have tried >>>>>> another mutation (just substitution of Asn to Lys) and I am getting >>>>>> the >>>>>> well-known >>>>>> >>>>>> "X particles communicated to PME node Y are more than a cell length >>>>>> out >>>>>> of >>>>>> the domain decomposition cell of their charge group" >>>>>> >>>>>> message error during energy minimization, right at the beginning (step >>>>>> 0). >>>>>> >>>>>> My energy minimization mdp file looks as follows: >>>>>> >>>>>> >>>>>> integrator = steep ; >>>>>> emtol = 1000.0; >>>>>> emstep = 0.02 ; >>>>>> nsteps = 7 ; >>>>>> nstlist = 1 ; >>>>>> ns_type = grid; >>>>>> rlist = 1.0 ; >>>>>> coulombtype = PME ; >>>>>> rcoulomb= 1.0; >>>>>> rvdw= 1.0 ; >>>>>> pbc = xyz; >>>>>> >>>>>> >>>>>> I have tried without neutralizing with ions, changing the time step, >>>>>> changing the integrator and the values for rcoulomb,rlist, etc. >>>>>> >>>>> >>>>> Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. >>>>> Changing >>>>> them will actually increase your likelihood of failure. >>>>> >>>>> I have changed all the parameteres in the mdp file and I get a smaller >>>>>> value of particles in the message error, but still a crash. >>>>>> The box size has also no effect on the message error. >>>>>> I have checked the starting structure and everything is fine. Mutating >>>>>> that >>>>>> Asn to a non-charged residue does not yield any problem, but I want to >>>>>> study the effect in the Asn--> Lys mutation. >>>>>&
Re: [gmx-users] X particles communicated to PME node Y are more ...
The version I was using this morning was 4.6 2013/3/4, Justin Lemkul : > > > On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote: >> I have tried the same issue (same system with same mdp file and same >> initial configuration as starting structure) and is running without >> any problems with GROMACS-4.5.5. >> >> Anyone knows what is happening? >> > > You didn't tell us your Gromacs version in the previous post so the best > guess > is "random bug that was somehow fixed before 4.5.5." > > -Justin > >> >> 2013/3/4, Justin Lemkul : >>> >>> >>> On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: >>>> Dear gmx users, >>>> >>>> I have successfully performed simulations on a charged peptide. I did a >>>> series of mutations and everything had a happy end. Now I have tried >>>> another mutation (just substitution of Asn to Lys) and I am getting the >>>> well-known >>>> >>>> "X particles communicated to PME node Y are more than a cell length out >>>> of >>>> the domain decomposition cell of their charge group" >>>> >>>> message error during energy minimization, right at the beginning (step >>>> 0). >>>> >>>> My energy minimization mdp file looks as follows: >>>> >>>> >>>> integrator = steep ; >>>> emtol = 1000.0; >>>> emstep = 0.02 ; >>>> nsteps = 7 ; >>>> nstlist = 1 ; >>>> ns_type = grid; >>>> rlist = 1.0 ; >>>> coulombtype = PME ; >>>> rcoulomb= 1.0; >>>> rvdw= 1.0 ; >>>> pbc = xyz; >>>> >>>> >>>> I have tried without neutralizing with ions, changing the time step, >>>> changing the integrator and the values for rcoulomb,rlist, etc. >>> >>> Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. >>> Changing >>> them will actually increase your likelihood of failure. >>> >>>> I have changed all the parameteres in the mdp file and I get a smaller >>>> value of particles in the message error, but still a crash. >>>> The box size has also no effect on the message error. >>>> I have checked the starting structure and everything is fine. Mutating >>>> that >>>> Asn to a non-charged residue does not yield any problem, but I want to >>>> study the effect in the Asn--> Lys mutation. >>>> >>>> Any hint to solve the error? >>>> >>> >>> If EM stops at the first step, there's usually something >>> catastrophically >>> wrong >>> with the starting configuration. If you've decreased the value of >>> emstep, >>> there's little else that will account for such behavior. >>> >>> -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] X particles communicated to PME node Y are more ...
I have tried the same issue (same system with same mdp file and same initial configuration as starting structure) and is running without any problems with GROMACS-4.5.5. Anyone knows what is happening? 2013/3/4, Justin Lemkul : > > > On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: >> Dear gmx users, >> >> I have successfully performed simulations on a charged peptide. I did a >> series of mutations and everything had a happy end. Now I have tried >> another mutation (just substitution of Asn to Lys) and I am getting the >> well-known >> >> "X particles communicated to PME node Y are more than a cell length out >> of >> the domain decomposition cell of their charge group" >> >> message error during energy minimization, right at the beginning (step >> 0). >> >> My energy minimization mdp file looks as follows: >> >> >> integrator = steep ; >> emtol = 1000.0; >> emstep = 0.02 ; >> nsteps = 7 ; >> nstlist = 1 ; >> ns_type = grid; >> rlist = 1.0 ; >> coulombtype = PME ; >> rcoulomb= 1.0; >> rvdw= 1.0 ; >> pbc = xyz; >> >> >> I have tried without neutralizing with ions, changing the time step, >> changing the integrator and the values for rcoulomb,rlist, etc. > > Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. > Changing > them will actually increase your likelihood of failure. > >> I have changed all the parameteres in the mdp file and I get a smaller >> value of particles in the message error, but still a crash. >> The box size has also no effect on the message error. >> I have checked the starting structure and everything is fine. Mutating >> that >> Asn to a non-charged residue does not yield any problem, but I want to >> study the effect in the Asn--> Lys mutation. >> >> Any hint to solve the error? >> > > If EM stops at the first step, there's usually something catastrophically > wrong > with the starting configuration. If you've decreased the value of emstep, > there's little else that will account for such behavior. > > -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
[gmx-users] X particles communicated to PME node Y are more ...
Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0; emstep = 0.02 ; nsteps = 7 ; nstlist = 1 ; ns_type = grid; rlist = 1.0 ; coulombtype = PME ; rcoulomb= 1.0; rvdw= 1.0 ; pbc = xyz; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn--> Lys mutation. Any hint to solve the error? -- 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] do_dssp
Hi Erik, Since I read in the mailing list that nobody had asked about 2.1.0, just decided to try an older version before going into the trouble itself... Kind of coward, I know, but the troubles with that version are already reported so that I thought things would be easier :) Thank-you a lot for your comments 2013/3/1 Erik Marklund > Interesting. Perhaps there are new issues with 2.1.0. Did you try to > execute the command yourself? > > Erik > > > On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote: > > The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it >> works >> fine. However, when converting the xpm to eps I get I plot very small, >> where one barely can see the colour code and the legend is sooo big. Does >> anyone know how to change that? >> >> >> >> >> >> 2013/3/1 Erik Marklund >> >> What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX >>> -o ddR1HavD) in your terminal? >>> >>> >>> Erik >>> >>> On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: >>> >>> I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you >>> got: >>> >>>> >>>> dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2> >>>> /dev/null' >>>> Reading frame 0 time0.000 >>>> Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# >>>> >>>> --- >>>> Program do_dssp, VERSION 4.6 >>>> Source code file: /usr/local/bin/gromacs-4.6/ >>>> src/tools/gmx_do_dssp.c, >>>> >>>> line: >>>> 667 >>>> >>>> Fatal error: >>>> Failed to execute command: Try specifying your dssp version with the >>>> -ver >>>> option. >>>> >>>> How can I fix that? >>>> >>>> Thanks >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> 2013/1/15 James Starlight >>>> >>>> Justin, thanks both options works perfect. >>>> >>>>> >>>>> >>>>> James >>>>> >>>>> 2013/1/15 Justin Lemkul : >>>>> >>>>> >>>>>> >>>>>> On 1/15/13 7:13 AM, James Starlight wrote: >>>>>> >>>>>> >>>>>>> Justin, >>>>>>> >>>>>>> >>>>>>> I want to obtain timescale on X as well as number of residues on Y >>>>>>> on the xmp graph . By default that graph has not legend so it's hard >>>>>>> to analyse it . >>>>>>> >>>>>>> >>>>>>> The legends are printed in the .xvg header. I've never had a >>>>>> problem >>>>>> plotting its contents (though they are usually somewhat unclear when >>>>>> >>>>>> plotted >>>>> >>>>> together) with xmgrace -nxy scount.xvg >>>>>> >>>>>> >>>>>> By the way have you forced with some problems with dppc ? Simetimes >>>>>> >>>>>>> I've obtain error like >>>>>>> >>>>>>> >>>>>>> There are 286 residues in your selected group >>>>>>> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2> >>>>>>> /dev/null' >>>>>>> Reading frame 0 time0.000 >>>>>>> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 >>>>>>> >>>>>>> >>>>>>> Fatal error: >>>>>>> Failed to execute command: Try specifying your dssp version with the >>>>>>> -ver option. >>>>>>> >>>>>>> and I dont know how to fix it. >>>>>>> >>>>>>> I'm using gromacs-4.6-beta 3 with dssp 2.0.3 >>>>>>> >>>>>>> >>>>>>> Since dssp changed its command line options, Gromacs had to adapt as >>>>>> >>>>>> well. >>>>> >>>>> The error tells you to use the -ver option; you should do so. >>>>>> Version 2 >>>>>
Re: [gmx-users] do_dssp
The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? 2013/3/1 Erik Marklund > What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX > -o ddR1HavD) in your terminal? > > > Erik > > On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: > > I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: >> >> dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2> >> /dev/null' >> Reading frame 0 time0.000 >> Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# >> >> --**- >> Program do_dssp, VERSION 4.6 >> Source code file: /usr/local/bin/gromacs-4.6/**src/tools/gmx_do_dssp.c, >> line: >> 667 >> >> Fatal error: >> Failed to execute command: Try specifying your dssp version with the -ver >> option. >> >> How can I fix that? >> >> Thanks >> >> >> >> >> >> >> >> 2013/1/15 James Starlight >> >> Justin, thanks both options works perfect. >>> >>> >>> James >>> >>> 2013/1/15 Justin Lemkul : >>> >>>> >>>> >>>> On 1/15/13 7:13 AM, James Starlight wrote: >>>> >>>>> >>>>> Justin, >>>>> >>>>> >>>>> I want to obtain timescale on X as well as number of residues on Y >>>>> on the xmp graph . By default that graph has not legend so it's hard >>>>> to analyse it . >>>>> >>>>> >>>> The legends are printed in the .xvg header. I've never had a problem >>>> plotting its contents (though they are usually somewhat unclear when >>>> >>> plotted >>> >>>> together) with xmgrace -nxy scount.xvg >>>> >>>> >>>> By the way have you forced with some problems with dppc ? Simetimes >>>>> I've obtain error like >>>>> >>>>> >>>>> There are 286 residues in your selected group >>>>> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2> >>>>> /dev/null' >>>>> Reading frame 0 time0.000 >>>>> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 >>>>> >>>>> >>>>> Fatal error: >>>>> Failed to execute command: Try specifying your dssp version with the >>>>> -ver option. >>>>> >>>>> and I dont know how to fix it. >>>>> >>>>> I'm using gromacs-4.6-beta 3 with dssp 2.0.3 >>>>> >>>>> >>>> Since dssp changed its command line options, Gromacs had to adapt as >>>> >>> well. >>> >>>> The error tells you to use the -ver option; you should do so. Version 2 >>>> should be the default, so check to make sure you're actually using that >>>> version and not the old dssp. >>>> >>>> >>>> -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-u
[gmx-users] do_dssp with 4.6
Dear gmx users, Has anyone tried dssp-2.1.0 with gromacs-4.6? I am having the common problems that were supossed not to be in the new releases -- 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] do_dssp
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2> /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight > Justin, thanks both options works perfect. > > > James > > 2013/1/15 Justin Lemkul : > > > > > > On 1/15/13 7:13 AM, James Starlight wrote: > >> > >> Justin, > >> > >> > >> I want to obtain timescale on X as well as number of residues on Y > >> on the xmp graph . By default that graph has not legend so it's hard > >> to analyse it . > >> > > > > The legends are printed in the .xvg header. I've never had a problem > > plotting its contents (though they are usually somewhat unclear when > plotted > > together) with xmgrace -nxy scount.xvg > > > > > >> By the way have you forced with some problems with dppc ? Simetimes > >> I've obtain error like > >> > >> > >> There are 286 residues in your selected group > >> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2> > >> /dev/null' > >> Reading frame 0 time0.000 > >> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 > >> > >> > >> Fatal error: > >> Failed to execute command: Try specifying your dssp version with the > >> -ver option. > >> > >> and I dont know how to fix it. > >> > >> I'm using gromacs-4.6-beta 3 with dssp 2.0.3 > >> > > > > Since dssp changed its command line options, Gromacs had to adapt as > well. > > The error tells you to use the -ver option; you should do so. Version 2 > > should be the default, so check to make sure you're actually using that > > version and not the old dssp. > > > > > > -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 > -- 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 g_hbond
The donors are two H atoms from the amide group of Gln residues. Thus, I will try the -merge option. Thank for the comment. I wonder if the following issue is affecting gromacs 4.5.5: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html 2013/1/11, Justin Lemkul : > > > On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote: >> Hi all, >> >> When calculating the average number of hbonds during a simulation, does >> the >> program g_hbond contemplate the possibility of an atom involved in two >> hbond? >> If I visualize the structures with molden, setting the same cutoff >> criterion for hbonding than g_hbond utilizes, I found out that some O >> atoms >> are forming two H bonds with two different hydrogen atoms at once. Other >> O >> atoms are forming just one H bond. >> >> With g_hbond I get the same average on systems when the same O atoms are >> forming two hbonds and in those where they form just one. >> >> If the criterion is just a cutoff distance and angle, I guess I should >> have >> seen the differences when using g_hbond with -num, but this never >> happened... Any clue? >> > > For O atoms with two putative H-bonds, are the donors on separate functional > > groups or molecules? If they are not, g_hbond considers them the same, > since > that is the default behavior of the -merge option. If you specify -nomerge, > > then the two hydrogen bonds will be considered distinct. > > -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
[gmx-users] about g_hbond
Hi all, When calculating the average number of hbonds during a simulation, does the program g_hbond contemplate the possibility of an atom involved in two hbond? If I visualize the structures with molden, setting the same cutoff criterion for hbonding than g_hbond utilizes, I found out that some O atoms are forming two H bonds with two different hydrogen atoms at once. Other O atoms are forming just one H bond. With g_hbond I get the same average on systems when the same O atoms are forming two hbonds and in those where they form just one. If the criterion is just a cutoff distance and angle, I guess I should have seen the differences when using g_hbond with -num, but this never happened... Any clue? -- 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 g_hbond
Hi all, When calculating the average number of hbonds during a simulation, does the program g_hbond contemplate the possibility of an atom involved in two hbond? If I visualize the structures with molden, setting the same cutoff criterion for hbonding than g_hbond utilizes, I found out that some O atoms are forming two H bonds with two different hydrogen atoms at once. Other O atoms are forming just one H bond. With g_hbond I get the same average on systems when the same O atoms are forming two hbonds and in those where they form just one. If the criterion is just a cutoff distance and angle, I guess I should have seen the differences when using g_hbond with -num, but this never happened... Any clue? -- 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] martian thing
Dear gmx users, Something very weird is happening with a .gro file and I wonder if any user has ever experienced something similar... I am doing umbrella sampling simulation on a peptide with capped termini residues (ACE and NH2). As starting structure for the pulling simulations I used the last frame from a 150 ns simulation, in order to asses the stability of my system before the umbrella procedure. I did NVT and NPT equilibration, and then the MD run. Then I extracted the last frame of that 150 ns run and placed it into an appropriate box for the pulling, so I run again editconf, genbox and energy minimization. Then at the equilibration step the weird thing came: in the .gro file I have the ACE residues written as NH2 in one of the chains! The atom names remain as they have to according to the force field nomenclature (CH3, HH31, HH32, ...) for this ACE of this chain, but it is name as NH2!!! This is happening only in this .gro file at this step. Everything is fine in the first equilibrations, the MD run, the energy minimization in the newbox... It just shows up after this equilibration. I wonder if I may just change NH2 to ACE where it is to be or it has to be with something more complicated. -- 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] Steered MD
You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not implemented in GROMACS (hope anyone corrects me if I am wrong) 2012/6/4 Mike M > Dear Gromacs Users, > > I am trying to study the conformational path from state A to state B with > targeted molecular dynamics. These two states are two different structures > of a peptide that I have calculated after a series of nmr experiments. I > have perform 100ns simulations separately of the two peptides to assess > their stabilty over the course of the simulations, but now I wonder how can > I direct my system A towards the state named as B. In the manual I have > read what it is said in the manual about this topic and the usage of -rb to > provide the coordinates of the B state, but I did not find out how to > properly set the simulation. > > Has anyone done this before? > > Thanks, > Mike > > -- > 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
