Re: [gmx-users] problem with genion
Hi Gurpreet, You probably performed energy minimization without a box, without PBC. Then you generated a box using editconf. That's where the PBC comes in. With genbox you fill the thing with solvent, and running grompp then will provide you a run input file, which is set up to be used for a simulation. That means, that molecules are shifted such that they are properly arranged with respect to the reference box, which does not need to correspond with what you think is the proper arrangement (i.e. all components together more or less in the center of the box). Exercise: Take the run input file you use as input for genion and convert it to .gro/.pdb for viewing (using editconf -f -o). Compare it with the structure you used as input to grompp. Be sure also to visualize the box and work out the shifts over the lattice (box) vectors. Tsjerk On 7/16/07, gurpreet singh <[EMAIL PROTECTED]> wrote: Thanks Tsjerk I referred the mail about the broken molecules but there the problem is i think somewhat different. in that case broken molecules are coming becasue of the PBC . since PBC is being used that is why some part of the molecule is coming from the other side of box and its looking as if protein is broken but in my case i think the situation is different, first of all i have not still started using the PBC in the simulation and my full molecule (broken molecule) is right in the center of the box. moreover i am getting this problem before starting any simulation. till i did some simulation in vaccum before adding ions , it went fine there and then while shifting to the water simulation i added ions and right after adding the ions my molecule is getting broken. Thanks With Regards Gurpreet 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Gurpreet, > > I didn't ask whether you used PBC, I suggested it was due to PBC. > Check the archives for "broken molecules" and such. > > Tsjerk > > On 7/16/07, gurpreet singh < [EMAIL PROTECTED]> wrote: > > Thanks Tsjerk for you reply > > i did not get your point . i think you are asking me whether i used PBC or > > not , so i want to tell you that the .tpr file which i used for genion > > command was created without using PBC. > > > > but will it make any difference ? > > > > Thanks > > With Regards > > Gurpreet > > > > On 7/16/07, Tsjerk Wassenaar < [EMAIL PROTECTED] > wrote: > > > > > > Gurpreet, > > > > > > > my system was going fine at that time but when i used the genion > > command to > > > > add ions , i found that my protein was broken into parts. > > > > what could be the reason for this ? > > > > > > PBC? > > > > > > > While running the genion it usually asked for the group into which we > > want > > > > to add the ions so i have checked with both the SOL group and OTH group > > > > seperatly , in both the cases ions were replacing the solvent molecules. > > Is > > > > their any way by which we can add ions without replacing any solvent > > > > molecules ? > > > > > > No, there's no space to put them. > > > Well, you could try to squeeze them in here or there manually, and > > > perform energy minimization... > > > > > > Cheers, > > > > > > Tsjerk > > > > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > Junior UD (post-doc) > > > Biomolecular NMR, Bijvoet Center > > > Utrecht University > > > Padualaan 8 > > > 3584 CH Utrecht > > > The Netherlands > > > P: +31-30-2539931 > > > F: +31-30-2537623 > > > ___ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing lis
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
Hi Arneh, I'd sort of do the same, but would use R (http://cran.r-project.org/) :) Just a matter of taste (and of sticking to free, open-source software). Tsjerk On 7/17/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: ok, thanks. I like Chris's suggestion. I'll try using matlab to parse it out (b/c matlab can easily ingest column formatted data), Arneh Tsjerk Wassenaar wrote: > Hi Arneh, > > I think you're out of luck here. However, this is an excellent > exercise to get started with writing custom made analysis tools :) > Alternatively, you could output the coordinates for the C and O using > g_traj and use a script to calculate the angles with the z-axis, in > case it's a single bond you're interested in. > > Cheers, > > Tsjerk > > On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: >> Hi, >> >> Looking through the gmx tools . . . was wondering, which tool would one >> use (if such a tool exists) to measure the fluctuation of a user-defined >> angle in a trajectory. >> >> For instance, I want to measure the angle defined by a carbonyl vector >> (a vector going through a C=O bond) in my molecule and the z-axis of the >> simulation box. How do I define this angle, and which tool would I use >> to measure it in each frame of my trr? >> >> Thanks, >> >> Arneh >> >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
ok, thanks. I like Chris's suggestion. I'll try using matlab to parse it out (b/c matlab can easily ingest column formatted data), Arneh Tsjerk Wassenaar wrote: Hi Arneh, I think you're out of luck here. However, this is an excellent exercise to get started with writing custom made analysis tools :) Alternatively, you could output the coordinates for the C and O using g_traj and use a script to calculate the angles with the z-axis, in case it's a single bond you're interested in. Cheers, Tsjerk On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: Hi, Looking through the gmx tools . . . was wondering, which tool would one use (if such a tool exists) to measure the fluctuation of a user-defined angle in a trajectory. For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. How do I define this angle, and which tool would I use to measure it in each frame of my trr? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] What if there are multi-definition of dihedrals?
Hi, All, If there are multi-definitions of the same dihedral in topology file, how will gromacs treat it? Using the second one, or the addition of the two items? The reason for my asking this is: a dihedral potential function like the following needs to be realized , V = sum(Cn*cos(phi)^n), n=1, 2, 3, 4, 5, 6. But the RB function in gromacs is limited for n up to 5. If multi-definition is considered as addition, the potential function can be splitted into two, one using RB function and the other using proper dihedral funciton with n=6. If not, can anyone recommend one solution? Thanks. Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units
If i understand correctly then rlist is the short range cutoff inside which the forces on the atoms are calculated every step (and the neighbour list is updated every nstlist steps). If you specify a value of rvdw or rcoulomb larger than rlist then the forces on the atoms between rlist and rvdw/rcoulomb are re-calculated only every nstlist steps (and again the neighbour list is updated every nstlist steps). However it does not make sense to do this for rcoulomb when using PME because if you did this then forces inside rlist and outside rcoulomb would be updated every step but for outside rlist and inside rcoulomb only updated every nstlist steps, so for PME rcoulomb should equal rlist. I think this is correct but i am sure someone will tell me if it is not. Tom --On Monday, July 16, 2007 06:56:41 -0400 Frankie Montenegro <[EMAIL PROTECTED]> wrote: Hi guys, My first question is with regards to the size relationship between rlist and rvdw/rcoulomb, and consequently the meaning of rlist. I found an excellent question on this exact same subject posted couple of years ago, but I couldn't find the answer to it. I copy parts of the question here, and I would greatly appreciate some comments. It's rather long, so I tried to cut and paste parts of it that are relevant to me. Quote: [gmx-users] again, rlist vs rvdw vs rcoulomb and something about energy groups m b mic0404 at yahoo.com Fri Jul 25 04:32:00 CEST 2003 dear all, I do MD simulations using a cutoff for both VdW and Coulomb interactions. I am rather confused about the parameters used in the input file. (rlist, rvdw, rcoulomb) cut-- Normally I would assume that if one uses a neighbour list there are (at least) two cutoffs: One for a sphere around each atom with ALL (and only) the atoms in this sphere considered when calculating the energy and the forces on the primary atom at EACH time step (rvdw, rcoulomb ?). A second (larger) cutoff that is used when calculating the neighbour-list at intervals of each 10 (or so) time steps (rlist ?) were of course rlist > rvdw and rcoulomb. If one uses a switched potential there is a third cutoff (the onset of the switching function) that would be shorter than rvdw and rcoulomb. this implies: rlist > rvdw,rcoulomb > r*_switch ... in contrast to (part of) the manual, and the errormsg given by the code. --cut-- In my calculations I now let rlist < rvdw, rcoulomb, to evade the error message that Gromacs gives me otherwise, but if what I wrote above is true then the physical implications would be a bit worrying ... and if I have rlist = rvdw, rcoulomb would that not mean that the neighbour list has to be re-calculated at each time-step to get consistant results ? So the question is: is what I wrote above correct or not ? and if not, what is the precise meaning of these parameters (rlist, rvdw, etc) End of Quote. My second question I am trying to minimize a model binary Lennard-Jones system. It is a cubic box, side length 5 sigmas (so, the size is in reduced units, sigma=1).I have two atom types, so I followed the manual and set sigma_ii = epsilon_ii = 1 for one atom type. I set rlist=1, but grompp_d complaines that "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist." Now, it seems to me that, if sigma_ii = 1, all lengths values in the mdp file (such as rlist) will be in units of sigma. Am I right here? r*=r/sigma=r/1=r, right? If so, why is grompp complaining about the size which is less then a quarter of the box? (At first I thought it is complaining about rlist being too small.) So, in conclusion, I either don't understand: A) meaning of the size of rlist, B) conversion to reduced units, C) quite possibly both. Here is my potential, if that can be of any help. PE_ij=sigma_ij^6 * [ 16.0* epsilon_ij / R_ij^6 - 12.0 * epsilon_ij * r_ij^2 / R_ij^8 - 4.0 * epsilon_ij / r_ij^6 ] +sigma_ij^12 * [-28.0 * epsilon_ij / R_ij^12 +24.0*epsilon_ij * r_ij ^2/ R_ij^14 + 4.0 * epsilon_ij / r_ij^12 ] where R_ij= const * sigma_ij is the cutoff for each of the three interactions. Thanks for your help, Frankie ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] Uni
Re: [gmx-users] Problems about sigma & epsilon to C6 & C12
You should get identical plots. I think rule 1 and rule 3 are equivalent. On 7/16/07, Janne Hirvi <[EMAIL PROTECTED]> wrote: Hello! Could you please help me to understand solution as well? I just plotted these functions so that I combined sigma and epsilon values using rule 3 sigma(ij)=(sigma(i)*sigma(j))^(1/2) epsilon(ij)=(epsilon(i)*epsilon(j))^(1/2) and corresponding C6 (4*epsilon*sigma^6) and C12 (4*epsilon*sigma^12) values using rule 1 C6(ij)=(C6(i)*C6(j))^(1/2) C12(ij)=(C12(i)*C12(j))^(1/2) and got identical plots. What I have missed? Janne > > My problem has solved. Finally I realized that my calculation is wrong. > Thank you so much! > > On 7/15/07, james zhang <[EMAIL PROTECTED]> wrote: > > > > From equation 5.3 page 88, I think rule 1 and 3 are equivalent if you > > convert the parameters. > > I am sorry. What's the different between rule 1 and 3? > > I think C6/C12 are used in rule 1 and sigma/epsilon are used in rule 3. > > But if you convert sigma/epsilon to C6/C12, these two should be > equivalent. > > I am confused. Can I convert sigma/epsilon to C6/C12 if I want to use gmx > > force field instead of OPLS ? > > Thanks. > > > > On 7/15/07, David van der Spoel < [EMAIL PROTECTED]> wrote: > > > > > > james zhang wrote: > > > > I used rule 3 for ffopls rule 1 for ffgmx. > > > > > > > please read the manual.these combination rules are not equivalent. > > > > > > there is also combination rule 2, see 5.3.3 > > > -- > > > David. > > > > > > > > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > > > Dept. of Cell and Molecular Biology, Uppsala University. > > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > > phone: 46 18 471 4205 fax: 46 18 511 755 > > > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > > > > > > > > > ___ > > > gmx-users mailing listgmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours, James Jianzhang Department of Mechanical and Chemical Engineering North Carolina Agricultural and Technical State University 1601 East Market Street Greensboro, NC 27411 [EMAIL PROTECTED] or [EMAIL PROTECTED] http://www.ncat.edu/~jzhang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parameters of hydrogen peroxide H2O2
Dear gmx-users, does anyone know if there are reasonable parameters for hydorgen peroxide H2O2 around? I found few references that present parameters for H2O2 via google, but in none of the cases it was clear to me where the parameters come from exactly and whether they have been tested properly. Thanks a lot in advance, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] free energy calculation and constraint distance?
Hello, What I want to do is calculate the free energy difference of pulling the ligand away from the receptor. I want to do it using theromdynamic intergration using the Lamda 0/1 stuff. I am just not clear of the procedure of how to do it. I want to constraint several distances between the ligand and the receptor and then increase that distance for state B(lamda=1)where the ligand and receptor are completely separated. For that, I would have to modify my topology where i define [ constraints ] for the distances i want to constrain between the ligand and the receptor and input the bond length for state A(lamda=0) and state B (lamda=1) for each. will the distances defined move the whole ligand away from the receptor? since am only defining several distances between ligand and receptor only. I want to make sure that my procedure above is correct for thermodynamic integeration. hope this clearifies what I am trying to say. Belquis > Sorry, I really didn't get, what your goal is and what, in fact, you > really want to do. > > For free energy calculations, you can > - either do Thermodynamic integration (the lambda 0/1 stuff) > - or pulling (force probe) and afterwards use Jarzynskis theorem > - or umbrella sampling together with WHAM (if I remember correctly) > > Now, it's up to you, which method you favormay also depend on your > system/question > > Regards > > Maik Goette, Dipl. Biol. > Max Planck Institute for Biophysical Chemistry > Theoretical & computational biophysics department > Am Fassberg 11 > 37077 Goettingen > Germany > Tel. : ++49 551 201 2310 > Fax : ++49 551 201 2302 > Email : mgoette[at]mpi-bpc.mpg.de > mgoette2[at]gwdg.de > WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ > > > [EMAIL PROTECTED] wrote: >> Hello Gromacs users, >> >> I am trying to do a free energy calculation, which I have never done >> before. I have read the manual and the tutorial on the wiki but there >> is >> still some issues not clear to me. >> >> I am trying to calculate free energy difference of pulling the ligand >> from >> a beta-sheet receptor. I understand there is a pull code with different >> options or it can be done with constraint distances. >> >> Please correct me if my procedure is wrong: I want to constraint >> several >> distances between the ligand and the receptor and then increase that >> distance to one where the ligand and receptor are completely separated. >> For that, I would have to modify my topology where i define [ >> constraints >> ] for the distances i want to constrain between the ligand and the >> receptor and input the bond length for state A(lamda=0) and state B >> (lamda=1) for each. >> >> will the distances defined move the whole ligand away from the >> receptor? >> since am only defining several distances between ligand and receptor >> only. >> >> or is it recommended to use the pull code? >> >> Any directions is appreciated. >> >> Belquis >> >> ___ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> . >> > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Regarding polymer equillibration (pressure changes)
Jeroen van Bemmelen wrote: Hi Ann, So my first question is wether this can be possible or not? or am I doing something wrong? if so, then how can i rectify the same error? I think you should definitely use 'editconf -density' to rescale your simulation box to the right density. editconf automatically rescales the box vectors AND the coordinates, so you won't have the problem of atom coordinates suddenly being larger than the box vectors. But anyhow it seems a bit weird to me that you're coordinates are so much larger than your box vectors (4.3 versus 3.4 nm). Perhaps this is related to the long molecule chains in combination with pbc? I'm not sure, maybe one of the developers can comment on this. How long are your chains? If more than 0.9 nm then this can happen. I think the fluctuations are okay and admittable.but the change in pressure averages make me confused. If I am right, at equillibrium all the observables (temp, pressure, density) should average around a steady value with some fluctuations. but the change in averages (pressure) makes me confused. I have read from literature that the equillibriation of polymers is comparitively diffcult. Fluctuations in the average pressure do not necessarily mean there's a equilibration problem, depending on the time it takes for the average pressure to converge for your system. Simply a matter of statistics. Since the pressure is always fluctuating enormously and converging slowly compared to other observables, I don't think that (only) checking the average pressure is a good way of determining whether a system is equilibrated or not. Of course, a drift in the average pressure could mean that your system is not equilibrated. But in that case you'd probably also see a significantly large drift in other observables, especially the potential energy and partial potential energy terms in your case. Cheers, Jeroen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Regarding polymer equillibration (pressure changes)
Hi Ann, > So my first question is > > wether this can be possible or not? or am I doing something wrong? > if so, then how can i rectify the same error? I think you should definitely use 'editconf -density' to rescale your simulation box to the right density. editconf automatically rescales the box vectors AND the coordinates, so you won't have the problem of atom coordinates suddenly being larger than the box vectors. But anyhow it seems a bit weird to me that you're coordinates are so much larger than your box vectors (4.3 versus 3.4 nm). Perhaps this is related to the long molecule chains in combination with pbc? I'm not sure, maybe one of the developers can comment on this. > I think the fluctuations are okay and admittable.but the change in pressure > averages make me confused. > > If I am right, at equillibrium all the observables (temp, pressure, density) > should average around a steady value with some fluctuations. but the change > in averages (pressure) makes me confused. I have read from literature that > the equillibriation of polymers is comparitively diffcult. Fluctuations in the average pressure do not necessarily mean there's a equilibration problem, depending on the time it takes for the average pressure to converge for your system. Simply a matter of statistics. Since the pressure is always fluctuating enormously and converging slowly compared to other observables, I don't think that (only) checking the average pressure is a good way of determining whether a system is equilibrated or not. Of course, a drift in the average pressure could mean that your system is not equilibrated. But in that case you'd probably also see a significantly large drift in other observables, especially the potential energy and partial potential energy terms in your case. Cheers, Jeroen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Segmentation fault after dt=2fs
Mahnam a écrit : In God We Trust Hello Dear Dr David van der Spoel Thank you for your quick response. I had used constraints before md simulation. I have done energy minimization and position restraint (20ps) (with constraints=all bonds )and then md simulation at 100 K, 200K and 300K for 100ps (with constraint=none) and then I extended my simulation at 300K for 700ps (e.g. 1000ps md simulation) with time step 1fs and everything is ok, only if I change time step to 2fs, it crashes. In order to use 2 ps time steps, you need to constrain the h-bonded interactions, using "h-bonds" instead of none should solve you problem. Consider also coupling counter-ions and solvent as mentionned by Justin A. Lemkul. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Segmentation fault after dt=2fs
Mahnam a écrit : In God We Trust Hello Dear Dr David van der Spoel Thank you for your quick response. I had used constraints before md simulation. I have done energy minimization and position restraint (20ps) (with constraints=all bonds )and then md simulation at 100 K, 200K and 300K for 100ps (with constraint=none) and then I extended my simulation at 300K for 700ps (e.g. 1000ps md simulation) with time step 1fs and everything is ok, only if I change time step to 2fs, it crashes. In order to use 2 ps time steps, you need to constrain the h-bonded interactions, using "h-bonds" instead of none should solve you problem. Consider also coupling counter-ions and solvent as mentionned by Justin A. Lemkul. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
SeungPyo Hong a écrit : Dear gmx-users, Recently I want to perform MD for protein with implicit solvent model. Gromacs does not seem to support it. Could you let me know where to find information about implicit solvent simulation with Gromacs? Also I will be glad if you tell me your opinion about the implicit solvent simulation to protein. Thank you. There is no Generalised-Born approach implemented (at least available) but you may consider reaction field. See chapter 7, paragraph "Electrostatics and VdW". Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units
From: "Frankie Montenegro" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users Subject: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion,and b) reduced units Date: Mon, 16 Jul 2007 06:56:41 -0400 Hi guys, My first question is with regards to the size relationship between rlist and rvdw/rcoulomb, and consequently the meaning of rlist. There are three options in Gromacs. The option you want is rcoulomb < rlist and rvdw < rlist. This works and gives the most accurate and also the most costly integration. A faster and very commonly used setting is: rlist=rcoulomb=rvdw. With PME the Coulomb interactions are very small at the cut-off, as are the LJ interactions. So with a small sacrifice in integration accuracy one can gain a lot of performance, also because analytical LJ is cheaper than tabulated. The last option is rcoulomb > rlist and/or rvdw > rlist. Then the energies and forces beyond rlist are only updated every nslist steps. This gives less integration accuracy but can give a lot of "interaction" accuracy at a small computational cost. My second question I am trying to minimize a model binary Lennard-Jones system. It is a cubic box, side length 5 sigmas (so, the size is in reduced units, sigma=1).I have two atom types, so I followed the manual and set sigma_ii = epsilon_ii = 1 for one atom type. I set rlist=1, but grompp_d complaines that "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist." Now, it seems to me that, if sigma_ii = 1, all lengths values in the mdp file (such as rlist) will be in units of sigma. Am I right here? r*=r/sigma=r/1=r, right? If so, why is grompp complaining about the size which is less then a quarter of the box? (At first I thought it is complaining about rlist being too small.) So, in conclusion, I either don't understand: A) meaning of the size of rlist, B) conversion to reduced units, C) quite possibly both. Here is my potential, if that can be of any help. PE_ij=sigma_ij^6 * [ 16.0* epsilon_ij / R_ij^6 - 12.0 * epsilon_ij * r_ij^2 / R_ij^8 - 4.0 * epsilon_ij / r_ij^6 ] +sigma_ij^12 * [-28.0 * epsilon_ij / R_ij^12 +24.0*epsilon_ij * r_ij ^2/ R_ij^14 + 4.0 * epsilon_ij / r_ij^12 ] where R_ij= const * sigma_ij is the cutoff for each of the three interactions. Thanks for your help, Frankie In Gromacs the units that you put in are the units you get out. The only exceptions are temperature, which involves the Boltzmann constant and pressure, which involves a factor of 16.6. So if you box size is 5 (as you say) and your cut-off is 1, then you should not get an error. So one of the two things is wrong. Maybe you made a pdb file with box 5? pdb is in Angstrom, while Gromacs uses nm, so there is a conversion factor of 0.1. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Regarding polymer equillibration (pressure changes )
Hi Gromacs crew and others I have a few questions regarding the equilibration of the system my system is linear PPG (polyprpylene glycol)polymer chain (melts in vaccum) with the following details number of monomers = 22 Total number of atoms = 3664 total number of chains = 16 My chains are aranged in a cubical box and growing along the y axis (crystal)with an initial box length of 10 10 10 along the three axes. Then I perfored a 0.5ns NPT simulation with the mdp parameters as follows integrator = md dt = 0.001 nsteps = 50 comm_mode= linear nstcomm = 1 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 500 nstenergy= 500 nstxtcout= 1 xtc_precision= 1 nstlist = 10 ns_type = grid pbc = xyz rlist= 0.9 coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.1 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes vdwtype = cut-off rvdw = 1.2 tcoupl = nose-hoover tc-grps = system tau_t= 0.5 ref_t= 450 Pcoupl = berendsen pcoupltype = isotropic tau_p= 2.0 compressibility = 4.5e-5 ref_p= 650.0 annealing= no gen_vel = no gen_temp = 500 gen_seed = 173529 morse= no constraints = none constraint_algorithm = lincs unconstrained_start = no lincs_order = 4 lincs_iter = 1 Avergaes over the run were as follows with fluctuations pressure = 355.327 (fluctutaion = around 700) Temperature = 450.001 density = 659.956 box length = 3.31199 Then I performed a 5ns NPT simulation with the above parametes in mdp file but with change in ref_p as 10bar. The averges afer the run were as follows with fluctuations pressure = 10.4371 (fluctutaion = around 700) Temperature = 450 density = 916.781 box length = 3.36644 (final gro file) Then i switched over to 5ns NVT by switching off the pressure coupling. As the box lenght was fluctuating i took the average of box lenghth (3.37275)and manually edited the final gro file from the NPT run and performed the NVT simulation. But there were some (MANY) coordinates that were greater than the above boxlength. as given below PPG H340 2433 4.174 2.456 0.903 1.8080 1.7019 -0.2709 PPG H341 2434 4.274 2.476 1.047 -1.0495 -1.9389 2.3833 PPG H342 2435 4.140 2.591 1.014 So my first question is wether this can be possible or not? or am I doing something wrong? if so, then how can i rectify the same error? The averages after the run were as follows pressure = 18.06 (fluctutaion = 802.807) Temperature = 450 density = 927.262 (calculated using "g_density -f traj.xtc -s NVT_5ns.tpr -sl 1") box length = 3.37275 (final gro file) is the g_density command as given in the brackets will give the correct density of my system ? if no, then what is the option that i have to set for the same ? Is the change in pressure and density okay? or is there something going wrong? Then i extended the above NVT simulation to 5ns more to observe the change in energy averages and was found to be as follows pressure = 28.5734 (fluctutaion = 802.807) Temperature = 450 (fluctutaion = 7.72976) density = 927.263 (calculated using "g_density -f traj.xtc -s NVT_10ns.tpr -sl 1") box length = 3.37275 (final gro file) why there can be an increase in pressure? does that means that my system is not equilibriated? if so how can i make my system at equillibrium? I think the fluctuations are okay and admittable.but the change in pressure averages make me confused. If I am right, at equillibrium all the observables (temp, pressure, density) should average around a steady value with some fluctuations. but the change in averages (pressure) makes me confused. I have read from literature that the equillibriation of polymers is comparitively diffcult. Thanking you in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with genion
Thanks Tsjerk I referred the mail about the broken molecules but there the problem is i think somewhat different. in that case broken molecules are coming becasue of the PBC . since PBC is being used that is why some part of the molecule is coming from the other side of box and its looking as if protein is broken but in my case i think the situation is different, first of all i have not still started using the PBC in the simulation and my full molecule (broken molecule) is right in the center of the box. moreover i am getting this problem before starting any simulation. till i did some simulation in vaccum before adding ions , it went fine there and then while shifting to the water simulation i added ions and right after adding the ions my molecule is getting broken. Thanks With Regards Gurpreet 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Gurpreet, I didn't ask whether you used PBC, I suggested it was due to PBC. Check the archives for "broken molecules" and such. Tsjerk On 7/16/07, gurpreet singh <[EMAIL PROTECTED]> wrote: > Thanks Tsjerk for you reply > i did not get your point . i think you are asking me whether i used PBC or > not , so i want to tell you that the .tpr file which i used for genion > command was created without using PBC. > > but will it make any difference ? > > Thanks > With Regards > Gurpreet > > On 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED] > wrote: > > > > Gurpreet, > > > > > my system was going fine at that time but when i used the genion > command to > > > add ions , i found that my protein was broken into parts. > > > what could be the reason for this ? > > > > PBC? > > > > > While running the genion it usually asked for the group into which we > want > > > to add the ions so i have checked with both the SOL group and OTH group > > > seperatly , in both the cases ions were replacing the solvent molecules. > Is > > > their any way by which we can add ions without replacing any solvent > > > molecules ? > > > > No, there's no space to put them. > > Well, you could try to squeeze them in here or there manually, and > > perform energy minimization... > > > > Cheers, > > > > Tsjerk > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > Junior UD (post-doc) > > Biomolecular NMR, Bijvoet Center > > Utrecht University > > Padualaan 8 > > 3584 CH Utrecht > > The Netherlands > > P: +31-30-2539931 > > F: +31-30-2537623 > > ___ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units
Hi guys, My first question is with regards to the size relationship between rlist and rvdw/rcoulomb, and consequently the meaning of rlist. I found an excellent question on this exact same subject posted couple of years ago, but I couldn't find the answer to it. I copy parts of the question here, and I would greatly appreciate some comments. It's rather long, so I tried to cut and paste parts of it that are relevant to me. Quote: [gmx-users] again, rlist vs rvdw vs rcoulomb and something about energy groups m b mic0404 at yahoo.com Fri Jul 25 04:32:00 CEST 2003 dear all, I do MD simulations using a cutoff for both VdW and Coulomb interactions. I am rather confused about the parameters used in the input file. (rlist, rvdw, rcoulomb) cut-- Normally I would assume that if one uses a neighbour list there are (at least) two cutoffs: One for a sphere around each atom with ALL (and only) the atoms in this sphere considered when calculating the energy and the forces on the primary atom at EACH time step (rvdw, rcoulomb ?). A second (larger) cutoff that is used when calculating the neighbour-list at intervals of each 10 (or so) time steps (rlist ?) were of course rlist > rvdw and rcoulomb. If one uses a switched potential there is a third cutoff (the onset of the switching function) that would be shorter than rvdw and rcoulomb. this implies: rlist > rvdw,rcoulomb > r*_switch ... in contrast to (part of) the manual, and the errormsg given by the code. --cut-- In my calculations I now let rlist < rvdw, rcoulomb, to evade the error message that Gromacs gives me otherwise, but if what I wrote above is true then the physical implications would be a bit worrying ... and if I have rlist = rvdw, rcoulomb would that not mean that the neighbour list has to be re-calculated at each time-step to get consistant results ? So the question is: is what I wrote above correct or not ? and if not, what is the precise meaning of these parameters (rlist, rvdw, etc) End of Quote. My second question I am trying to minimize a model binary Lennard-Jones system. It is a cubic box, side length 5 sigmas (so, the size is in reduced units, sigma=1).I have two atom types, so I followed the manual and set sigma_ii = epsilon_ii = 1 for one atom type. I set rlist=1, but grompp_d complaines that "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist." Now, it seems to me that, if sigma_ii = 1, all lengths values in the mdp file (such as rlist) will be in units of sigma. Am I right here? r*=r/sigma=r/1=r, right? If so, why is grompp complaining about the size which is less then a quarter of the box? (At first I thought it is complaining about rlist being too small.) So, in conclusion, I either don't understand: A) meaning of the size of rlist, B) conversion to reduced units, C) quite possibly both. Here is my potential, if that can be of any help. PE_ij=sigma_ij^6 * [ 16.0* epsilon_ij / R_ij^6 - 12.0 * epsilon_ij * r_ij^2 / R_ij^8 - 4.0 * epsilon_ij / r_ij^6 ] +sigma_ij^12 * [-28.0 * epsilon_ij / R_ij^12 +24.0*epsilon_ij * r_ij ^2/ R_ij^14 + 4.0 * epsilon_ij / r_ij^12 ] where R_ij= const * sigma_ij is the cutoff for each of the three interactions. Thanks for your help, Frankie ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hi guys, My first question is with regards to the size relationship between rlist and rvdw/rcoulomb, and consequently the meaning of rlist. I found an excellent question on this exact same subject posted couple of years ago, but I couldn't find the answer to it. I copy parts of the question here, and I would greatly appreciate some comments. It's rather long, so I tried to cut and paste parts of it that are relevant to me. Quote: [gmx-users] again, rlist vs rvdw vs rcoulomb and something about energy groups m b mic0404 at yahoo.com Fri Jul 25 04:32:00 CEST 2003 dear all, I do MD simulations using a cutoff for both VdW and Coulomb interactions. I am rather confused about the parameters used in the input file. (rlist, rvdw, rcoulomb) cut-- Normally I would assume that if one uses a neighbour list there are (at least) two cutoffs: One for a sphere around each atom with ALL (and only) the atoms in this sphere considered when calculating the energy and the forces on the primary atom at EACH time step (rvdw, rcoulomb ?). A second (larger) cutoff that is used when calculating the neighbour-list at intervals of each 10 (or so) time steps (rlist ?) were of course rlist > rvdw and rcoulomb. If one uses a switched potential there is a third cutoff (the onset of the switching function) that would be shorter than rvdw and rcoulomb. this implies: rlist > rvdw,rcoulomb > r*_switch ... in contrast to (part of) the manual, and the errormsg given by the code. --cut-- In my calculations I now let rlist < rvdw, rcoulomb, to evade the error message that Gromacs gives me otherwise, but if what I wrote above is true then the physical implications would be a bit worrying ... and if I have rlist = rvdw, rcoulomb would that not mean that the neighbour list has to be re-calculated at each time-step to get consistant results ? So the question is: is what I wrote above correct or not ? and if not, what is the precise meaning of these parameters (rlist, rvdw, etc) End of Quote. My second question I am trying to minimize a model binary Lennard-Jones system. It is a cubic box, side length 5 sigmas (so, the size is in reduced units, sigma=1).I have two atom types, so I followed the manual and set sigma_ii = epsilon_ii = 1 for one atom type. I set rlist=1, but grompp_d complaines that "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist." Now, it seems to me that, if sigma_ii = 1, all lengths values in the mdp file (such as rlist) will be in units of sigma. Am I right here? r*=r/sigma=r/1=r, right? If so, why is grompp complaining about the size which is less then a quarter of the box? (At first I thought it is complaining about rlist being too small.) So, in conclusion, I either don't understand: A) meaning of the size of rlist, B) conversion to reduced units, C) quite possibly both. Here is my potential, if that can be of any help. PE_ij=sigma_ij^6 * [ 16.0* epsilon_ij / R_ij^6 - 12.0 * epsilon_ij * r_ij^2 / R_ij^8 - 4.0 * epsilon_ij / r_ij^6 ] +sigma_ij^12 * [-28.0 * epsilon_ij / R_ij^12 +24.0*epsilon_ij * r_ij ^2/ R_ij^14 + 4.0 * epsilon_ij / r_ij^12 ] where R_ij= const * sigma_ij is the cutoff for each of the three interactions. Thanks for your help, Frankie ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] free energy calculation and constraint distance?
Sorry, I really didn't get, what your goal is and what, in fact, you really want to do. For free energy calculations, you can - either do Thermodynamic integration (the lambda 0/1 stuff) - or pulling (force probe) and afterwards use Jarzynskis theorem - or umbrella sampling together with WHAM (if I remember correctly) Now, it's up to you, which method you favormay also depend on your system/question Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hello Gromacs users, I am trying to do a free energy calculation, which I have never done before. I have read the manual and the tutorial on the wiki but there is still some issues not clear to me. I am trying to calculate free energy difference of pulling the ligand from a beta-sheet receptor. I understand there is a pull code with different options or it can be done with constraint distances. Please correct me if my procedure is wrong: I want to constraint several distances between the ligand and the receptor and then increase that distance to one where the ligand and receptor are completely separated. For that, I would have to modify my topology where i define [ constraints ] for the distances i want to constrain between the ligand and the receptor and input the bond length for state A(lamda=0) and state B (lamda=1) for each. will the distances defined move the whole ligand away from the receptor? since am only defining several distances between ligand and receptor only. or is it recommended to use the pull code? Any directions is appreciated. Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with genion
Gurpreet, I didn't ask whether you used PBC, I suggested it was due to PBC. Check the archives for "broken molecules" and such. Tsjerk On 7/16/07, gurpreet singh <[EMAIL PROTECTED]> wrote: Thanks Tsjerk for you reply i did not get your point . i think you are asking me whether i used PBC or not , so i want to tell you that the .tpr file which i used for genion command was created without using PBC. but will it make any difference ? Thanks With Regards Gurpreet On 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED] > wrote: > > Gurpreet, > > > my system was going fine at that time but when i used the genion command to > > add ions , i found that my protein was broken into parts. > > what could be the reason for this ? > > PBC? > > > While running the genion it usually asked for the group into which we want > > to add the ions so i have checked with both the SOL group and OTH group > > seperatly , in both the cases ions were replacing the solvent molecules. Is > > their any way by which we can add ions without replacing any solvent > > molecules ? > > No, there's no space to put them. > Well, you could try to squeeze them in here or there manually, and > perform energy minimization... > > Cheers, > > Tsjerk > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > ___ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with genion
Thanks Tsjerk for you reply i did not get your point . i think you are asking me whether i used PBC or not , so i want to tell you that the .tpr file which i used for genion command was created without using PBC. but will it make any difference ? Thanks With Regards Gurpreet On 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Gurpreet, > my system was going fine at that time but when i used the genion command to > add ions , i found that my protein was broken into parts. > what could be the reason for this ? PBC? > While running the genion it usually asked for the group into which we want > to add the ions so i have checked with both the SOL group and OTH group > seperatly , in both the cases ions were replacing the solvent molecules. Is > their any way by which we can add ions without replacing any solvent > molecules ? No, there's no space to put them. Well, you could try to squeeze them in here or there manually, and perform energy minimization... Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems about sigma & epsilon to C6 & C12
Hello! Could you please help me to understand solution as well? I just plotted these functions so that I combined sigma and epsilon values using rule 3 sigma(ij)=(sigma(i)*sigma(j))^(1/2) epsilon(ij)=(epsilon(i)*epsilon(j))^(1/2) and corresponding C6 (4*epsilon*sigma^6) and C12 (4*epsilon*sigma^12) values using rule 1 C6(ij)=(C6(i)*C6(j))^(1/2) C12(ij)=(C12(i)*C12(j))^(1/2) and got identical plots. What I have missed? Janne > > My problem has solved. Finally I realized that my calculation is wrong. > Thank you so much! > > On 7/15/07, james zhang <[EMAIL PROTECTED]> wrote: > > > > From equation 5.3 page 88, I think rule 1 and 3 are equivalent if you > > convert the parameters. > > I am sorry. What's the different between rule 1 and 3? > > I think C6/C12 are used in rule 1 and sigma/epsilon are used in rule 3. > > But if you convert sigma/epsilon to C6/C12, these two should be > equivalent. > > I am confused. Can I convert sigma/epsilon to C6/C12 if I want to use gmx > > force field instead of OPLS ? > > Thanks. > > > > On 7/15/07, David van der Spoel < [EMAIL PROTECTED]> wrote: > > > > > > james zhang wrote: > > > > I used rule 3 for ffopls rule 1 for ffgmx. > > > > > > > please read the manual.these combination rules are not equivalent. > > > > > > there is also combination rule 2, see 5.3.3 > > > -- > > > David. > > > > > > > > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > > > Dept. of Cell and Molecular Biology, Uppsala University. > > > Husargatan 3, Box 596, 75124 Uppsala, Sweden > > > phone: 46 18 471 4205 fax: 46 18 511 755 > > > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > > > > > > > > > ___ > > > gmx-users mailing listgmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > > > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Implicit solvent simulation
Dear gmx-users, Recently I want to perform MD for protein with implicit solvent model. Gromacs does not seem to support it. Could you let me know where to find information about implicit solvent simulation with Gromacs? Also I will be glad if you tell me your opinion about the implicit solvent simulation to protein. Thank you. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with genion
Gurpreet, my system was going fine at that time but when i used the genion command to add ions , i found that my protein was broken into parts. what could be the reason for this ? PBC? While running the genion it usually asked for the group into which we want to add the ions so i have checked with both the SOL group and OTH group seperatly , in both the cases ions were replacing the solvent molecules. Is their any way by which we can add ions without replacing any solvent molecules ? No, there's no space to put them. Well, you could try to squeeze them in here or there manually, and perform energy minimization... Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with genbox
Hi Mark, From the log it seems you're trying to solvate your protein (-cp gmx.pdb) with your protein (-cs gmx.gro)! Read the manual on genbox... Tsjerk On 7/16/07, Mark Zottola <[EMAIL PROTECTED]> wrote: I am trying to run genbox and am getting a segmentation fault. After running pdg2gmx, I generated a gro file from the pdb outfput from pdb2gmx using editconf. I then ran the editconf which seemed to run without problem. Then I tried to use genbox. It was at this point I received a segmentation fault. I have attached the log file from genbox. As I am new user to Gromacs, I am trying to follow the spider toxin tutorial for my protein. Any hints or pointers would be welcome. Thanks! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Magic number error
Hi Fernando, Did you try using version 3.2 yourself? Tsjerk On 7/14/07, zazeri <[EMAIL PROTECTED]> wrote: Hi to all! :D I'm facing a problem with the xtc file. It has been getting me the following error: Program trjconv, VERSION 3.3.1 Source code file: xtcio.c, line: 83 Fatal error: Magic Number Error in XTC file (read 0, should be 1995). In the mailing list I've found a person who said installing the gromacs version 3.2 the problem was solved. (I'm using 3.3 version) Could somebody confirm it for me ? Maybe could it be the case of correcting the code in xtcio.c ? And how should it be? Thanks in advance! Fernando Lopes Dept. of Physics UNESP - São José do Rio Preto - SP - Brazil Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] which tool to use a measure a user-defined angle in a traj
Hi Arneh, I think you're out of luck here. However, this is an excellent exercise to get started with writing custom made analysis tools :) Alternatively, you could output the coordinates for the C and O using g_traj and use a script to calculate the angles with the z-axis, in case it's a single bond you're interested in. Cheers, Tsjerk On 7/13/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote: Hi, Looking through the gmx tools . . . was wondering, which tool would one use (if such a tool exists) to measure the fluctuation of a user-defined angle in a trajectory. For instance, I want to measure the angle defined by a carbonyl vector (a vector going through a C=O bond) in my molecule and the z-axis of the simulation box. How do I define this angle, and which tool would I use to measure it in each frame of my trr? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
