Re: [gmx-users] Binding Copper to Protein
Hi, Justin raises a number of problems, but there's another one. Copper is a transition metal with a specific coordination which depends on the oxidation state. If you only use bonds, you sort of assume that the coordination geometry is the result of a size-exclusion effect. In this respect, copper is to be regarded an exotic species: http://wiki.gromacs.org/index.php/Exotic_Species Cheers, Tsjerk On Sat, Mar 21, 2009 at 1:05 PM, Justin A. Lemkul wrote: > > > DimitryASuplatov wrote: >> >> Hello, >> I am working with enzyme that contains Cu2+ in the active site. During a >> free simulation it always gets out due to minor conformational changes >> of coordinating residues. Since the copper is known to be essential for >> enzyme catalysis I want to set some extra force to bind it to certain >> residues. >> >> 1/ I have not found CU2+ in opls ff. In ions.itp CU is defined as CU2+ >> atomtype which I think is taken from GMX ff. Is it correct to use GMX >> Copper parametrization with OPLS? >> > > If you are ever asking yourself, "Can I take part of one force field and > introduce it into another?" the answer is always *absolutely not.* > > However, CU2+ is part of OPLS (in ions.itp, there is CU2+ after #ifdef > _FF_OPLS), and a reference for these parameters is given in ffoplsaa.atp. > >> 2/ What is the easiest way to bind a metal ion to a histidine residue? >> What if I add the bond to specbonds.dat without changing HIS topology >> (dihedral can be set to 0 0 0 0 0 0 in the itp file of the protein)? Can >> this be correct? >> > > You can try it and see. Whether or not you think it's appropriate is going > to depend on what is known about your particular system. But if you are > defining a bonded interaction of any sort between a metal ion and an amino > acid side chain, I would argue that the original HIS topology is no longer > valid, since it is sharing electrons with the metal, thus affecting the > charge of all species involved in the bonded interaction. > > -Justin > >> Thanks. I appreciate your time. >> SDA >> >> ___ >> gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ___ > gmx-users mailing list gmx-us...@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 gmx-users-requ...@gromacs.org. > 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 59, Issue 138
Pawan Kumar wrote: Hello Justin Sir, Greetings from Pawan Thanks for your valuable suggestion and reply. Initially I gave the emtol of 1000 and the output I got was : Steepest Descents converged to machine precision in 163 steps but did not reach the requested Fmax<1000. Potential Energy = - 4.4516497e+05 ...and how close did Fmax get to 1000? Even I tried to minimize the popc bilayer which I took from Tieleman sir's website ( before generating a bigger bilayer using genconf ) but that also converged to machine precision but not to the requested Fmax<1000. How do I proceed further ? Well, these things are not absolute; Fmax = 1000 is kind of a rule of thumb that I use in my own work, but sometimes it is not necessary. Careful equilibration should massage your system into cooperating. -Justin Thanks for your suggestions and help. Thanking you, Pawan On Thu, Mar 19, 2009 at 9:13 PM, Pawan Kumar wrote: > Hello Justin Sir, > > Greetings from Pawan > Thanks for your valuable suggestion and reply. > After inserting the protein in the bilayer using genbox I have minimized > the whole system without using any position restraints (i.e. define = > -DFLEXIBLE in em.mdp file). I used vanderwaal's distance parameter ( > -vdwd of 0.6 ) in the genbox step. > After running mdrun for energy minimization I got the output as : > Steepest Descents converged to Fmax<2250 in 14 steps. > Potential energy = - 6.9484700e+05 > Maximum force = 2.2114819e+03 on atom 34277 > Norm. of force = 5.0103039e+04 > You should try for an Fmax of no greater than 1000. 2250 is still very high. > I tried decreasing the emtol value in the em.mdp file but it ended with > machine precision. How far did it converge? What was Fmax? > I have read in literature that 5000 steps of Steetest Descents run is > required after inserting the protein in the bilayer which should be > followed by atleast 1000 steps of conjugate gradients. How can I > accomplish this ? Is there any parameter to be given in the em.mdp file > ? I use steep as the integrator in the mdp file for energy minimization. Read the manual. Whether or not that exact setup is going to be "required" is likely system-specific. I would say that as long as your system converges to a stable, negative Epot with a reasonable Fmax (less than 1000, but ideally lower) then you *may* have an appropriate starting structure. -Justin > Please help with some suggestions. > Thanks in advance. > > Thanking you, > Pawan > > > ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation gromacs-3.2.1 in redhat-6
akalabya bissoyi wrote: hello everybody i am trying to install gromacs-3.2.1 in redhat-6 EP. but facing problem (missing --run autoheader). plz any body tell me how to install it. Several suggestions: 1. Post your command lines (at which step in installation are you stuck?) and the exact screen output 2. Google your problem, because it does not sound like a Gromacs problem, but rather something to do with (maybe?) autoconf. 3. Install the newest version of Gromacs (4.0.4), since 3.2.1 is archaic and substantially slower! 4. Make sure all of your compilers/libraries/headers, etc are up-to-date. Red Hat 6 is a bit outdated, IIRC. -Justin i am sending the terminal window massage. thank you in advance -- AKALABYA BISSOYI N.I.T.Rourkela ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138
Hello Justin Sir, Greetings from Pawan Thanks for your valuable suggestion and reply. Initially I gave the emtol of 1000 and the output I got was : Steepest Descents converged to machine precision in 163 steps but did not reach the requested Fmax<1000. Potential Energy = - 4.4516497e+05 Even I tried to minimize the popc bilayer which I took from Tieleman sir's website ( before generating a bigger bilayer using genconf ) but that also converged to machine precision but not to the requested Fmax<1000. How do I proceed further ? Thanks for your suggestions and help. Thanking you, Pawan On Thu, Mar 19, 2009 at 9:13 PM, > Pawan Kumar wrote: > > Hello Justin Sir, > > > > Greetings from Pawan > > Thanks for your valuable suggestion and reply. > > After inserting the protein in the bilayer using genbox I have minimized > > the whole system without using any position restraints (i.e. define = > > -DFLEXIBLE in em.mdp file). I used vanderwaal's distance parameter ( > > -vdwd of 0.6 ) in the genbox step. > > After running mdrun for energy minimization I got the output as : > > Steepest Descents converged to Fmax<2250 in 14 steps. > > Potential energy = - 6.9484700e+05 > > Maximum force = 2.2114819e+03 on atom 34277 > > Norm. of force = 5.0103039e+04 > > > > You should try for an Fmax of no greater than 1000. 2250 is still very > high. > > > I tried decreasing the emtol value in the em.mdp file but it ended with > > machine precision. > > How far did it converge? What was Fmax? > > > I have read in literature that 5000 steps of Steetest Descents run is > > required after inserting the protein in the bilayer which should be > > followed by atleast 1000 steps of conjugate gradients. How can I > > accomplish this ? Is there any parameter to be given in the em.mdp file > > ? I use steep as the integrator in the mdp file for energy minimization. > > Read the manual. > > Whether or not that exact setup is going to be "required" is likely > system-specific. I would say that as long as your system converges to a > stable, > negative Epot with a reasonable Fmax (less than 1000, but ideally lower) > then > you *may* have an appropriate starting structure. > > -Justin > > > Please help with some suggestions. > > Thanks in advance. > > > > Thanking you, > > Pawan > > > > > > > ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] installation gromacs-3.2.1 in redhat-6
hello everybody i am trying to install gromacs-3.2.1 in redhat-6 EP. but facing problem (missing --run autoheader). plz any body tell me how to install it. i am sending the terminal window massage. thank you in advance -- AKALABYA BISSOYI N.I.T.Rourkela log file(gromacs-3.2.1) Description: Binary data ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Non-equilibraium MD: simulating a moving plate.
Hello, I want to simulate a rigid plate (wall) moving along one direction and reflecting all the particles it meets. I have made a potential only for repulsion which acts at the distances less than 1 nm (and equals zero at bigger ones) and bound it to a particle. If the plate is immovable everything goes OK. To make it go I use acc-grps = WAL accelerate = 0 0 1 where the acceleration is in [nm/ps2] (from the gmx manual 4.0). To make a plate motion insensitive to the molecules it reflects, its mass was set to a very big value. But during the following run the plane moved very slowly while all other particles in the system have obtained an acceleration at the same direction. Even those ones which are to far to interact with a plate. Why? Then if the mass of the plate is reduced the above effect is not so pronounced but then the plate becomes very sensible to the interactions, so its motion is not as we want... If the acceleration is given in [nm/ps2], how the mass can influence the motion? I thought this value is just added to the value obtained from the interations, but it's evidently not true here. Please let me know if it's possible in gromacs to make such moving plate I described and if so, what is a good practice to simulate this effect? Thank you, Vitaly -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] One more broken .trr file
Sarah Witzke wrote: Dear gromacs users, I would very much appreciate it if anyone could give me an advice on the following situation: I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files each of ~0.2 ns (giving a total of 1098 small .trr files). There were no errors or otherwise "suspicious" behavior during the simulation. After the simulation I concatenated all the small .trr files into one big .trr file (version 4.0.2 to correspond with other simulations): trjcat -f *.trr -o dmpclim1-all.trr trjcat gave no error message, the last line output to the screen was: "last frame written was 219600.015625 ps" After the concatenation I checked the big .trr file with gmxcheck: gmxcheck -f dmpclim1-all.trr The result was: Checking file dmpclim1-all.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 35508 Reading frame 17000 time 17.016 Warning at frame 17379: coordinates for atom 10917 are large (-2.99061e+19) Warning at frame 17379: coordinates for atom 10921 are large (1.42767e+31) Warning at frame 17379: coordinates for atom 10925 are large (-1.29194e+13) Warning at frame 17379: coordinates for atom 10925 are large (1.51714e+34) Reading frame 21000 time 21.016 Item#frames Timestep (ps) Step 2196110 Time 2196110 Lambda 2196110 Coords 2196110 Velocities 2196110 Forces 0 Box 2196110 Frame 17379 is located in the small .trr file number 870. .trr file 870 consists of 22 frames and the error is in frame 20. Looking at dmpclim1-870.trr in VMD reveals that two water molecules are far, far away (as noted by gmxcheck) in frame 20. Both in frame 19 and in frame 21 the two waters are placed nicely in the box. The dmpclim1-870.log and the screen output from 870 are both normal (i.e. they look similar to all the other steps), so my guess is that something happened during writing to file? I remember a similar problem posted very recently: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Reading these emails I understand that there is no way to delete just a single frame - is that correct? When posting links, right-click the frame and open it in a new window/tab. Then you will have the link that actually points to the message you found. This link is just the search page :) I have thought about two possible options for me now: 1) Use the suggestion given by Justin Lemkul in the email mentioned: trjconv -f dmpclim1-870.trr -b 0 -e 19 -o xxx.trr This is guess would make me loose 3 frames corresponding to (0.2 ns/22)*3 = 0.027 ns. It's not a problem to have 0.027 ns less of simulation, but will it affect later on when I concatenate the small .trr files, convert them to an .xtc file, and then use that to calculate e.g. area/lipid or membrane thickness? Will there be a time-mismatch? Yes, you will likely get complaints from all the Gromacs tools in such a case. The other option is to uniformly cut out frames from all your .trr files (trjconv -skip), such that the bad frame would never appear, and you would have uniformly-spaced frames in all of your .trr files. That may be sacrificing quite a bit of data, however. 2) Redo step 870. I'm able to redo step 870 quite easily, but what will then happen when I try to concatenate all the small .trr files? I fear that the "old" -870.trr wouldn't be exactly identical to the "new" -870.trr (due to round-off) and that this would make a mismatch with -871.trr? If you have a checkpoint file, you should get a binary identical continuation. -Justin I'm very sorry to ask this kind of question again, but I hope you'll bear with me and have the patience to help me! Best regards, Sarah ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing
[gmx-users] Non-equilibraium MD: simulating a moving plate.
Hello, I want to simulate a rigid plate (wall) moving along one direction and reflecting all the particles it meets. I have made a potential only for repulsion which acts at the distances less than 1 nm (and equals zero at bigger ones) and bound it to a particle. If the plate is immovable everything goes OK. To make it go I use acc-grps = WAL accelerate = 0 0 1 where the acceleration is in [nm/ps2] (from the gmx manual 4.0). To make a plate motion insensitive to the molecules it reflects, its mass was set to a very big value. But during the following run the plane moved very slowly while all other particles in the system have obtained an acceleration at the same direction. Even those ones which are to far to interact with a plate. Why? Then if the mass of the plate is reduced the above effect is not so pronounced but then the plate becomes very sensible to the interactions, so its motion is not as we want... If the acceleration is given in [nm/ps2], how the mass can influence the motion? I thought this value is just added to the value obtained from the interations, but it's evidently not true here. Please let me know if it's possible in gromacs to make such moving plate I described and if so, what is a good practice to simulate this effect? Thanks you, Vitaly ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] One more broken .trr file
Dear gromacs users, I would very much appreciate it if anyone could give me an advice on the following situation: I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files each of ~0.2 ns (giving a total of 1098 small .trr files). There were no errors or otherwise "suspicious" behavior during the simulation. After the simulation I concatenated all the small .trr files into one big .trr file (version 4.0.2 to correspond with other simulations): trjcat -f *.trr -o dmpclim1-all.trr trjcat gave no error message, the last line output to the screen was: "last frame written was 219600.015625 ps" After the concatenation I checked the big .trr file with gmxcheck: gmxcheck -f dmpclim1-all.trr The result was: Checking file dmpclim1-all.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 35508 Reading frame 17000 time 17.016 Warning at frame 17379: coordinates for atom 10917 are large (-2.99061e+19) Warning at frame 17379: coordinates for atom 10921 are large (1.42767e+31) Warning at frame 17379: coordinates for atom 10925 are large (-1.29194e+13) Warning at frame 17379: coordinates for atom 10925 are large (1.51714e+34) Reading frame 21000 time 21.016 Item#frames Timestep (ps) Step 2196110 Time 2196110 Lambda 2196110 Coords 2196110 Velocities 2196110 Forces 0 Box 2196110 Frame 17379 is located in the small .trr file number 870. .trr file 870 consists of 22 frames and the error is in frame 20. Looking at dmpclim1-870.trr in VMD reveals that two water molecules are far, far away (as noted by gmxcheck) in frame 20. Both in frame 19 and in frame 21 the two waters are placed nicely in the box. The dmpclim1-870.log and the screen output from 870 are both normal (i.e. they look similar to all the other steps), so my guess is that something happened during writing to file? I remember a similar problem posted very recently: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Reading these emails I understand that there is no way to delete just a single frame - is that correct? I have thought about two possible options for me now: 1) Use the suggestion given by Justin Lemkul in the email mentioned: trjconv -f dmpclim1-870.trr -b 0 -e 19 -o xxx.trr This is guess would make me loose 3 frames corresponding to (0.2 ns/22)*3 = 0.027 ns. It's not a problem to have 0.027 ns less of simulation, but will it affect later on when I concatenate the small .trr files, convert them to an .xtc file, and then use that to calculate e.g. area/lipid or membrane thickness? Will there be a time-mismatch? 2) Redo step 870. I'm able to redo step 870 quite easily, but what will then happen when I try to concatenate all the small .trr files? I fear that the "old" -870.trr wouldn't be exactly identical to the "new" -870.trr (due to round-off) and that this would make a mismatch with -871.trr? I'm very sorry to ask this kind of question again, but I hope you'll bear with me and have the patience to help me! Best regards, Sarah ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Binding Copper to Protein
DimitryASuplatov wrote: Hello, I am working with enzyme that contains Cu2+ in the active site. During a free simulation it always gets out due to minor conformational changes of coordinating residues. Since the copper is known to be essential for enzyme catalysis I want to set some extra force to bind it to certain residues. 1/ I have not found CU2+ in opls ff. In ions.itp CU is defined as CU2+ atomtype which I think is taken from GMX ff. Is it correct to use GMX Copper parametrization with OPLS? If you are ever asking yourself, "Can I take part of one force field and introduce it into another?" the answer is always *absolutely not.* However, CU2+ is part of OPLS (in ions.itp, there is CU2+ after #ifdef _FF_OPLS), and a reference for these parameters is given in ffoplsaa.atp. 2/ What is the easiest way to bind a metal ion to a histidine residue? What if I add the bond to specbonds.dat without changing HIS topology (dihedral can be set to 0 0 0 0 0 0 in the itp file of the protein)? Can this be correct? You can try it and see. Whether or not you think it's appropriate is going to depend on what is known about your particular system. But if you are defining a bonded interaction of any sort between a metal ion and an amino acid side chain, I would argue that the original HIS topology is no longer valid, since it is sharing electrons with the metal, thus affecting the charge of all species involved in the bonded interaction. -Justin Thanks. I appreciate your time. SDA ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem in running simulation
nitu sharma wrote: Dear all, Thanks for solving my problems.But i have one new problem is I have to Insert my protein into dmpc lipid bilayer before doing simulation that bilayer file i got from teleman website can anybody help me in doing this process using gromacs-4.0.3. clue- I have , - protein pdb file -lipid pdb file . what should i have to do next using gromacs. There are a variety of ways to insert your protein. Many are described in the list archive (hint: search!) Another option (again available from Tieleman's site) is the InflateGRO program. -Justin please if anybody knows about that let me know its very critical problem for me. Thank you very much in advance. Nitu Sharma School of life Sciences Jawaherlal Nehru University New Delhi , India ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] nitu sharma has invited you to open a Google mail account
I've been using Gmail and thought you might like to try it out. Here's an invitation to create an account. --- nitu sharma has invited you to open a free Gmail account. To accept this invitation and register for your account, visit http://mail.google.com/mail/a-1cd37518c7-688f8e9f41-8e6ee8aa1c Once you create your account, nitu sharma will be notified with your new email address so you can stay in touch with Gmail! If you haven't already heard about Gmail, it's a new search-based webmail service that offers: - Over 2,700 megabytes (two gigabytes) of free storage - Built-in Google search that instantly finds any message you want - Automatic arrangement of messages and related replies into "conversations" - Powerful spam protection using innovative Google technology - No large, annoying ads--just small text ads and related pages that are relevant to the content of your messages To learn more about Gmail before registering, visit: http://mail.google.com/mail/help/benefits.html And, to see how easy it can be to switch to a new email service, check out our new switch guide: http://mail.google.com/mail/help/switch/ We're still working every day to improve Gmail, so we might ask for your comments and suggestions periodically. We hope you'll like Gmail. We do. And, it's only going to get better. Thanks, The Gmail Team (If clicking the URLs in this message does not work, copy and paste them into the address bar of your browser). ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem in running simulation
Dear all, Thanks for solving my problems.But i have one new problem is I have to Insert my protein into dmpc lipid bilayer before doing simulation that bilayer file i got from teleman website can anybody help me in doing this process using gromacs-4.0.3. clue- I have , - protein pdb file -lipid pdb file . what should i have to do next using gromacs. please if anybody knows about that let me know its very critical problem for me. Thank you very much in advance. Nitu Sharma School of life Sciences Jawaherlal Nehru University New Delhi , India ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_principal
Hello, sorry to ask again, but I wander if the output files (axis1.dat,axis2.dat and axis3.dat) of the g_principal program refer to Ixx, Ixy, Ixz, Iyx, Iyy, Iyz, Izx, Izy, Izz components respectively. Thank you Antonia _ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:how to get the the force plot after pulling
> Date: Thu, 19 Mar 2009 13:52:09 +0800 > From: huifang liu > Subject: [gmx-users] how to get the the force plot after pulling > dynamic simulation using GMX-3.3 > To: gmx-users@gromacs.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > I am recently doing a SMD. I think i did it very well. But i don't know how > to get the force plot. Is there some one can give me a suggestion? > Thank you very much. > At the end of the SMD you should have obtained a .pdo file. In that file the time and the coordinates of the reference- (R), pull-group (P) and of the spring (S) are written. If i remember correctly it was: t, Rx, Ry, Rz, Px, Sx, Py, Sy, Pz, Sz. If you have more pullgroups then you have first the x-coordinates of P and S, then y-coordinates ... (look in the manual or the header of the .pdo; or for t=0 you should know the position of all particals and springs and can calculate a little bit to see which entry corresponds to which group). Hi, Thomas, Thank you very much for your reply. It is really helpful to me. But there are two things that still confuse me. My .pdo file is like this: # AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group 'USK' # Nr. of pull groups 1 # Group 1 'UNK' afmVec -0.179258 0.695867 -0.695439 AfmRate 0.005000 AfmK 500.00 # 0.002.7391006.9843082.668408 4.0162774.0162802.0263862.026388 7.6232777.623278 0.0020002.7391006.9843082.668408 4.0162774.0162782.0263862.026394 7.6232777.623271 0.0040002.7391006.9843082.668408 4.0162774.0162762.0263862.026401 7.6232777.623264 0.0060002.7391006.9843082.668408 4.0162774.0162752.0263862.026408 7.6232777.623257 0.0080002.7391006.9843082.668408 4.0162774.0162732.0263862.026415 7.6232777.623250 0.012.7391006.9843082.668408 4.0162774.0162712.0263862.026422 7.6232777.623243 0.0120002.7391006.9843082.668408 4.0162774.0162692.0263862.026429 7.6232777.623236 0.0140002.7391006.9843082.668408 4.0162774.0162672.0263862.026436 7.6232777.623229 0.0160002.7391006.9843082.668408 4.0162774.0162662.0263862.026443 7.6232777.623222 0.0180002.7391006.9843082.668408 4.0162774.0162642.0263862.026450 7.6232777.623215 0.022.7391006.9843082.668408 4.0162774.0162622.0263862.026457 7.6232777.623208 0.0220002.7391006.9843082.668408 4.0162774.0162602.0263862.026464 7.6232777.623201 Since the column 5, 7, 9 only changed after every picosecond and column 6, 8,10 changed per 0.002 ps (i set the dt=0.002 in .mdp file). I am wondering whether the column 5,7,9 stand for Sx, Sy, Sz or Px, Py, Pz as you said. If you are right, why the Px, Py, Pz keep the same every picosecond? Is this beacuse that i set the nstxout=500 in the .mdp file (1ps=dt*nstxout). > > For the force-calculation: The force is the deflection of the spring > times the force-constant of the spring -> Fx = k(Sx-Px) ... for the > other directions it's analog. Then you can calculate the magnitude of F > and plot it against the time (if you are only interested in the > magnitude of force). Or you can calculate the force in the pulling > direction and plot it against time. If i want to calcutate the force in the pulling direction, F=sqrt(Fx*Fx+Fy*Fy+Fz*Fz) ? Thank you so much. Huifang > > > Hope this helps. > Thomas > > > Huifang > > > > -- > > Huifang Liu (Ph.D. Student) > > School of Pharmacy > > Fudan University > > > > 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) > > Shanghai, China, 200032 Cell phone: +86-13764669357 > > E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 > > -- next part -- > > An HTML attachment was scrubbed... > > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090319/2f249dff/attachment-0001.html > > > > -- > Huifang Liu (Ph.D. Student) > School of Pharmacy > Fudan University > > 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) > Shanghai, China, 200032 Cell phone: +86-13764669357 > E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 > ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] Simulated annealing
jayant james wrote: Hi ! I am attempting to do a simulated annealing and running into problem. Let me give a introduction to my system. I have a segment of a protein that was not crystallographyically resolved, but was later resolved by NMR. So I ligated the NMR structure to the crystal structure and in an attempt to find the correct orientation of the NMR segment in the crystal structure I planned to do a simulated annealing run specifically to this ligated NMR segment. Having ligated this NMR segment to the crystal structure I gave the pdb2gmx command, then created a box, filled it with water and performed a distance restrained energy minimization (wherein I input some FRET distances as distance restraints). Its all fine till this step. Now I create an index group that has the NMR group as the third group in the temperature coupling, the other two are Protein and Non-Protein. when I run the grompp to start a simulated annealing run I get a message stating that the NMR group's atoms are also found in the Protein group. Gromacs is right in detecting this problem. As I cannot have the same amino acids in 2 different groups which are coupled to two different temperatures. So how am I to attempt this simulated annealing because the program does not want to have the NMR group present in the Protein group? You will need to make special index groups, i.e.: r 1-x (for the appended segment) r x-y (the rest of the protein) These groups can be used as your tc-grps. -Justin So say I delete the NMR segment that was appended to the crystal structure how and which stage do I integrate the NMR group that I wanted to perform the simulated annealing on, into the system? Thanks Jayant *The pr.mdp file is as below* ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = Protein Non-Protein NMR-group tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein Non-ProteinNMR-group ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ; ; ; ;simulated annealing ;Type of annealing form each temperature group (no/single/periodic) annealing = nono single ; ;Number of annealing points to use for specifying annealing in each group annealing_npoints 0 0 9 ; ; List of times at the annealing points for each group annealing_time = 0 25 50 75 100 125 150 175 200 ; Temp.at each annealing point, for each group. annealing_temp = 300 350 400 450 500 450 400 350 300 *The error messge is given below* creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_D 1 Excluding 2 bonded neighbours for SOL 72948 Excluding 1 bonded neighbours for NA+ 214 Excluding 1 bonded neighbours for CL- 207 processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # G96BONDS: 4588 # G96ANGLES: 6638 # PDIHS: 2521 # IDIHS: 2044 # LJ14: 7634 # DISRES: 22 # SETTLE: 72948 initialising group options... processing index file... WARNING 1 [file "new.top", line 28039]: T-Coupling group Protein has fewer than 10% of the atoms (4550 out of 223817) Maybe you want to try Protein and Non-Protein instead? WARNING 2 [file "new.top", line 28039]: T-Coupling group Non-Protein has fewer than 10% of the atoms (2 out of 223817) Maybe you want to try Protein and Non-Protein instead? --- Program grompp, VERSION 3.3.3 Source code file: readir.c, line: 843 Fatal error: Atom 2589 in multiple T-Coupling groups (1 and 3) --- ** ** *The commands that I use are given below* ** #pdb2gmx -f start.pdb -p new -o new -ignh -merge #creating a box and addition of water molecules #editconf -f new.gro -o out -c -princ -d 2.2 #genbox -cp out -cs -o check #editconf -f check -o check.pdb #rasmol check.pdb #Energy minimization and addition of ions to neutralise the system #grompp -f em.mdp -c check -p new.top -o em.tpr #genion -s em.tpr -o next -p new -random -g -neutral -conc 0.15 #pname -Na -np 13 #editconf -f next.gro -o next.pdb #rasmol next.pdb #option 13 for SOL #Running the EM. Here change the Na to NA+ i
[gmx-users] Binding Copper to Protein
Hello, I am working with enzyme that contains Cu2+ in the active site. During a free simulation it always gets out due to minor conformational changes of coordinating residues. Since the copper is known to be essential for enzyme catalysis I want to set some extra force to bind it to certain residues. 1/ I have not found CU2+ in opls ff. In ions.itp CU is defined as CU2+ atomtype which I think is taken from GMX ff. Is it correct to use GMX Copper parametrization with OPLS? 2/ What is the easiest way to bind a metal ion to a histidine residue? What if I add the bond to specbonds.dat without changing HIS topology (dihedral can be set to 0 0 0 0 0 0 in the itp file of the protein)? Can this be correct? Thanks. I appreciate your time. SDA ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] One more broken .trr file
Dear gromacs users, I would very much appreciate it if anyone could give me an advice on the following situation: I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files each of ~0.2 ns (giving a total of 1098 small .trr files). There were no errors or otherwise "suspicious" behavior during the simulation. After the simulation I concatenated all the small .trr files into one big .trr file (version 4.0.2 to correspond with other simulations): trjcat -f *.trr -o dmpclim1-all.trr trjcat gave no error message, the last line output to the screen was: "last frame written was 219600.015625 ps" After the concatenation I checked the big .trr file with gmxcheck: gmxcheck -f dmpclim1-all.trr The result was: Checking file dmpclim1-all.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 35508 Reading frame 17000 time 17.016 Warning at frame 17379: coordinates for atom 10917 are large (-2.99061e+19) Warning at frame 17379: coordinates for atom 10921 are large (1.42767e+31) Warning at frame 17379: coordinates for atom 10925 are large (-1.29194e+13) Warning at frame 17379: coordinates for atom 10925 are large (1.51714e+34) Reading frame 21000 time 21.016 Item#frames Timestep (ps) Step 2196110 Time 2196110 Lambda 2196110 Coords 2196110 Velocities 2196110 Forces 0 Box 2196110 Frame 17379 is located in the small .trr file number 870. .trr file 870 consists of 22 frames and the error is in frame 20. Looking at dmpclim1-870.trr in VMD reveals that two water molecules are far, far away (as noted by gmxcheck) in frame 20. Both in frame 19 and in frame 21 the two waters are placed nicely in the box. The dmpclim1-870.log and the screen output from 870 are both normal (i.e. they look similar to all the other steps), so my guess is that something happened during writing to file? I remember a similar problem posted very recently: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Reading these emails I understand that there is no way to delete just a single frame - is that correct? I have thought about two possible options for me now: 1) Use the suggestion given by Justin Lemkul in the email mentioned: trjconv -f dmpclim1-870.trr -b 0 -e 19 -o xxx.trr This is guess would make me loose 3 frames corresponding to (0.2 ns/22)*3 = 0.027 ns. It's not a problem to have 0.027 ns less of simulation, but will it affect later on when I concatenate the small .trr files, convert them to an .xtc file, and then use that to calculate e.g. area/lipid or membrane thickness? Will there be a time-mismatch? 2) Redo step 870. I'm able to redo step 870 quite easily, but what will then happen when I try to concatenate all the small .trr files? I fear that the "old" -870.trr wouldn't be exactly identical to the "new" -870.trr (due to round-off) and that this would make a mismatch with -871.trr? I'm very sorry to ask this kind of question again, but I hope you'll bear with me and have the patience to help me! Best regards, Sarah ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Simulated annealing
Hi ! I am attempting to do a simulated annealing and running into problem. Let me give a introduction to my system. I have a segment of a protein that was not crystallographyically resolved, but was later resolved by NMR. So I ligated the NMR structure to the crystal structure and in an attempt to find the correct orientation of the NMR segment in the crystal structure I planned to do a simulated annealing run specifically to this ligated NMR segment. Having ligated this NMR segment to the crystal structure I gave the pdb2gmx command, then created a box, filled it with water and performed a distance restrained energy minimization (wherein I input some FRET distances as distance restraints). Its all fine till this step. Now I create an index group that has the NMR group as the third group in the temperature coupling, the other two are Protein and Non-Protein. when I run the grompp to start a simulated annealing run I get a message stating that the NMR group's atoms are also found in the Protein group. Gromacs is right in detecting this problem. As I cannot have the same amino acids in 2 different groups which are coupled to two different temperatures. So how am I to attempt this simulated annealing because the program does not want to have the NMR group present in the Protein group? So say I delete the NMR segment that was appended to the crystal structure how and which stage do I integrate the NMR group that I wanted to perform the simulated annealing on, into the system? Thanks Jayant *The pr.mdp file is as below* ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tc-grps = Protein Non-Protein NMR-group tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein Non-ProteinNMR-group ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ; ; ; ;simulated annealing ;Type of annealing form each temperature group (no/single/periodic) annealing = nono single ; ;Number of annealing points to use for specifying annealing in each group annealing_npoints 0 0 9 ; ; List of times at the annealing points for each group annealing_time = 0 25 50 75 100 125 150 175 200 ; Temp.at each annealing point, for each group. annealing_temp = 300 350 400 450 500 450 400 350 300 *The error messge is given below* creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_D 1 Excluding 2 bonded neighbours for SOL 72948 Excluding 1 bonded neighbours for NA+ 214 Excluding 1 bonded neighbours for CL- 207 processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # G96BONDS: 4588 # G96ANGLES: 6638 # PDIHS: 2521 # IDIHS: 2044 # LJ14: 7634 # DISRES: 22 # SETTLE: 72948 initialising group options... processing index file... WARNING 1 [file "new.top", line 28039]: T-Coupling group Protein has fewer than 10% of the atoms (4550 out of 223817) Maybe you want to try Protein and Non-Protein instead? WARNING 2 [file "new.top", line 28039]: T-Coupling group Non-Protein has fewer than 10% of the atoms (2 out of 223817) Maybe you want to try Protein and Non-Protein instead? --- Program grompp, VERSION 3.3.3 Source code file: readir.c, line: 843 Fatal error: Atom 2589 in multiple T-Coupling groups (1 and 3) --- ** ** *The commands that I use are given below* ** #pdb2gmx -f start.pdb -p new -o new -ignh -merge #creating a box and addition of water molecules #editconf -f new.gro -o out -c -princ -d 2.2 #genbox -cp out -cs -o check #editconf -f check -o check.pdb #rasmol check.pdb #Energy minimization and addition of ions to neutralise the system #grompp -f em.mdp -c check -p new.top -o em.tpr #genion -s em.tpr -o next -p new -random -g -neutral -conc 0.15 #pname -Na -np 13 #editconf -f next.gro -o next.pdb #rasmol next.pdb #option 13 for SOL #Running the EM. Here change the Na to NA+ in topology file and I/P *.gro file. #grompp -f em.mdp -c next.gro -p new.top -o em.tpr #mdrun -v -s em -x em -o em -c em.gro & #editconf -f em.gro -o em.pdb #rasmol em.pdb *This is where the problem begins* #Running MD. grompp -f pr.mdp -c em
RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems
Hello, thank you Mr Berk for your answers once again. Taking them as feedback and judging from my simulations, two more questions arise. I would be more than grateful if you could answer me the following: 1)you refer to an initial guess for the compressibility tensor of gromacs. As it was refered to a previous post, the best thing someone can have as an input is the linear compressibility, which as far as I know is a vector and not a tensor. I have found it as scalar modulus too. Taking it as a vector and consulting the book: Physical properties of crystals by J.F.Nye, I get this equation for beta: β= (s11+s12+s13)l1**2 + (s12+s22+s23)l2**2 + (s13+s23+s33)l3**2 with l1, l2, l3 the unit axis vectors and sxx the compliance tensor components. Now, judging from the above, the xy compressibility tensor component in your implementation in gromacs, should be something like the resultant of the components of beta in l1 and l2 direction (or if you prefer in x and y)? 2)You mention than if I have a liquid then PR anisotropic pressure coupling should be avoided because the box should deform a lot. No objection to this. My question though is: If I start from the crystal structure with anisotropic pressure coupling and want to melt it, how I should be able to conduct such an md knowing that the melt after a while should crash. I have to mention that It crashed either if I have an anisotropic melt md simulation or if I started from a crystal and melt that crystal. The message I get is: Not all bonded interactions have been properly assigned to the domain decomposition cells or Fatal error: The X-size of the box (1.808111) times the triclinic skew factor (0.989963) is smaller than the number of DD cells (2) times the smallest allowed cell size (0.895000) The independent simulations (anisotropic crystal, isotropic melt) face no problem. Thank you in advance, Nikos --- Berk Hess schrieb am Do, 19.3.2009: Von: Berk Hess Betreff: RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems An: "Discussion list for GROMACS users" Datum: Donnerstag, 19. März 2009, 12:43 Hi, You will have to come up yourself with a reasonable guess. If you have a hard crystal, I guess it would be close to the diagonal values. Note that with PR coupling tau_p has to be large enough, something like 10 ps. (note that in Gromacs 4.0 a bug has been corrected which scaled tau_p by 16..6 in version 3.3 and before) But for equilibration I would start with Berendsen. Berk Date: Thu, 19 Mar 2009 04:30:44 -0700 From: lastexile...@yahoo.de Subject: RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems To: gmx-users@gromacs.org Hello, I do have a crystal system. You refer to an initial guess. So if I understand correctly, it is a trial and error, if I do not have any data, this is what I can make out of. The part of the shear stress you are reffering I think that it is from experimental values? Now you say that : compressibility (real) = tau_p*compressibility (gromacs) ? If this is the case I do not think that the units coincide. (ps/bar) =? (1/bar) I think that what you mean has to do with equation 3.36 in the manual, where with these components the W is calculated. Forgive my ignorance in the issue. Thank you, Nikos --- Berk Hess schrieb am Do, 19.3.2009: Von: Berk Hess Betreff: RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems An: "Discussion list for GROMACS users" Datum: Donnerstag, 19. März 2009, 10:23 Hi, If you have a liquid system (no off-diagonal elasticity), you should not use full anistropic pressure coupling. If you have a solid system (for instance a crystal), you will have an elastic shear stress response and you can determine and use off-diagonal compressibility values. You need the compressibility values to set the time scale of the pressure coupling. The compressibility does not affect any thermodynamic quantity, only the dynamics. The compressibility always occurs as a product with 1/tau_p. If you want to determine them from a simulation, you need a reasonable initial guess for the compressibility and you can use a large tau_p to be on the safe side with the actual coupling time. Berk Date: Wed, 18 Mar 2009 16:02:38 -0700 From: lastexile...@yahoo.de To: gmx-users@gromacs.org Subject: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems Hello, Searching first the gromacs mailing list I could not find an answer to the problem I face. I would like to know the vaules I have to give to the mdp file where it asks for compressibility. I have to conduct an NPT simulation using barostat Parrinello-Rahman. My pressure coupling should be anisotropic. The values I have given up to now are: tau_p = 1.0 compressibility = 4..5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-
