[gmx-users] error oxo
Dear experts, Hi! I see the following on the site: Error 0x0 and 0x1 From FaHWiki Jump to: navigation, search The 0x0 and 0x1 errors are unknown errors - all errors that are known will end with some other error code and message, but those errors that Pande Group hasn't seen before or did not know about, will end with error 0x0 or 0x1. Note: The WU data of an unknown error can not be trusted and by definition you'll never get any credit for it. If the 0x0 and 0x1 error cause is identified and classified as some sort of EUE then you'll start getting credit for such WUs. One possible cause of errors 0x1 and 0x0 is a hardware failure (which is why the software is unable to classify them). If a RAM failure is detected by the OS or for some reason the program wishes to allocate more memory and the OS refuses, the OS will terminate FAHcore_* and the client will no longer be able to communicate with the FAHcore producing Client-core communications error: ERROR 0x1 0x0 errors are Unix Specific and under Linux this error often can be related to Glibc incompatibility. Note: When using the Gromacs core on Linux, this error is also generated in circumstances where the Windows core would produce a Gromacs Cannot Continue further EUE. Unfortunately Pandegroup are currently unsure how WUs are triggering this error. As a result a normal EUE is not triggered, and the whole WU gets dumped and lost. Folding-community: Guha Jayachandran's comment in Core status 0? Under the Gromacs33 (A0) core, this error is returned because even though the cause is known, it has not yet been categorised. The error creates an output in the log similar to this: Warning: 1-4 interaction between and at distance 0.000 which is larger than the 1-4 table size 8.298 nm One possible cause for error 0x0 is forgetting to redirect the standard output. If you're running in the background without a command such as './fah5 -verbosity 9 /dev/null 21 ', the simulation will probably get past 100% and then create an error. These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file It should be noted that you yourself cannot increase the table-extension, it is an integral part of the WU Error 0x1 is not always an unknown error When a WU expires, you may receive this error: As I have the Lincs error.Is my problem related to this type? As I am using Suse linux and I added directly the gromacs software to Installation packages. Regards, Lal badshah Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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] .itp file for polymer (Polystyrene)
Hi, I am trying to generate a polymer layer with 30 chains of 20 monomeric units using gromacs' genbox command. For that, I need to have .itp file for the single polymer chain (polystyrene). I have .itp file for styrene molecule, how can I make a .itp file for polymer chain using .itp file of styrene? I guess there must be some way to use parameters of styrene molecule to build up a .itp file for the polymer. I would appreciate If someone can help me with this. Many Thanks Rohit - Chat on a cool, new interface. No download required. Click here.___ 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] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours
An update: Using a 4th order PME spline resulted in ~ 15 % increase in efficiency. Thank you, Carsten. On Mon, Mar 24, 2008 at 3:08 PM, maria goranovic [EMAIL PROTECTED] wrote: Dear All, My apologies. I had too big a simulation cell, and too few atoms, hence the problem. No particular reason to choose order 5. I will try with pme_order 4 and see if it improves performance anyway. thanks ! -maria On Mon, Mar 24, 2008 at 2:19 PM, Carsten Kutzner [EMAIL PROTECTED] wrote: Am 24.03.2008 um 10:17 schrieb maria goranovic: Hi Folks, My simulation is running too slow. It took 10 wall clock hours (40 cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much larger systems (~ 16 atoms) using the same gromacs installation on the same hardware, and they run much faster than this (200 ps per 40 cpu hours). Can anybody suggest why this is happening ? Is it because of latency in the cpu communication? If so, what is the workaround ? Is there a special reason for using pme_order=5? I would use the default, 4 instead, or at least an even number. Carsten My .mdp script is below. These are the run commands. grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o heat.tpr mpirun -np 4 ~/bin/mdrun_mpi -np 4 -v -s heat.tpr -o heat.trr -c heat.gro -e heat -g heat.log heat.out ;### ; heat.mdp ; title = heating cpp = /usr/bin/cpp constraints = hbonds constraint_algorithm = lincs unconstrained_start = yes integrator = md nsteps = 25000 dt = 0.002 comm_mode = linear nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid pbc = xyz ; -- coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rlist = 1.0 rvdw= 1.0 fourierspacing = 0.1 pme_order = 5 ewald_rtol = 1e-5 ; --- ; Berendsen temperature and preasure coupling Tcoupl = berendsen tc-grps = DPPC SOL tau_t = 0.6 0.6 ; i have also tried a tau value of 0.1, but no speed up ref_t = 323.0 323.0 Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 1.01.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01.0 ; --- gen_vel = yes gen_temp= 323.0 gen_seed= 194040 ;### -- Maria G. Technical University of Denmark Copenhagen ___ 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 -- Maria G. Technical University of Denmark Copenhagen -- Maria G. Technical University of Denmark Copenhagen ___ 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] Error in equilibration
ewald_rtol = 1e5 I don't know if this is related or not, but ewald_rtol is, by default, 1e-5, so I suspect you've made a typo. -- step 0Warning: 1-4 interaction between 196 and 201 at distance 1.104 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Well, something's exploding, but you haven't given us any information about your system. To get more detailed help, you will have to tell us a little about what you are doing. What is in your system? What force field are you using? How did you prepare the system? Did the energy minimization step converge appropriately to a nice, negative potential energy? -Justin Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query about itp file of sugar
I wnt to generate an itp file for carbihydrate which contains a glucose,a galactose and a neuraminidase.I want to know which force fied to use and the the linkages to use for the sugar.Please let me know the way by which I can make the itp file for the sugar.Eagerly waiting for a reply, Shreya - Save all your chat conversations. Find them online.___ 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] Re: Hi
Please keep correspondence on the gmx-users listserv, so that an archived copy will be preserved for others to benefit from later. See my replies below. Quoting sudheer babu [EMAIL PROTECTED]: Hi Mr. Justin, Sorry for the posting my question to your personal mail, You made me clear so many doubts in gromacs , Thanks for that. But I have one doubt since one week trying get answer by different ways, but I didn't find, that is FF for protein in POPC. you replied me that read literature I read it. I found that using united atom FF( Berger) for lipid and all atom FF(OPLS) for protein, in case of membrane protein simulation,i tried to use in this way but it showing error, when I do minimisation I mentioned FF in .top in this way, Well, what is the error? It is of no use to say that something didn't work. What were you doing? What was the *exact* command you issued? What was the *exact* error message? Include forcefield parameters #include ffoplsaa.itp - for protein #include ffgmx.itp- for lipid #include lipid.itp #include popc.itp Right; this is a problem. Inclusion of both ffoplsaa.itp and ffgmx.itp will probably cause the two to fight. If you look through the list archives thoroughly, you will find an excellent procedure written by Chris Neale related to exactly how to do this. You may also want to refer to Chapter 5 of the manual for general information on topologies. Pls give me detail explanation and suggest, normally which FFs use when protein inserted into POPC Refer to the literature. I have seen papers that have used Gromos96 and OPLS-AA for membrane protein simulations. The choice is up to you, based on what you find and what you believe to be most applicable to your system. -Justin Thanks in advance. Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Informatin about Force field for Protein in POPC
Please keep this on the mailing list. I use OPLS + tip4p for protein in water, then I use the Berger lipids downloaded from Peter Tieleman's website using some special considerations for scaling of the 1-4 interactions. You can find some of my posts on that topic via searching for opls and berger. However, I work with beta-barrel proteins. If you are working on a helical protein (e.g. GPCRs) you may want to try amber, but I am not sure what lipids you would use there (the scaling trick doesn't work for amber-berger combo). Another way to go would be charmm with it's own lipids (as simulated in gromacs). The fundamental question of what protein ff you want is something that I can not answer for you. Chris. sudheer babu wrote: Hi Mr. Chris, This is Sudheer working as a project associate, I am working on membrane proteins I want to clarify one thing regarding force field in gromacs. Intially I want to simulate my protein in water, later insert to POPC bilayer. So my doubt is, protein in water which FF can use, later when embedded into POPC which FF can use for protein and POPC. Pls help me. I am waiting for reply Thanks 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
[gmx-users] POL3 polarizable water model
Dear Gromacs users, I wonder whether or not the POL3 polarizable water model (Caldwell JW, Kollman PA (1995) J Phys Chem 99: 6208-6219.) can be incorporated in gmx with amber03 force field. Thanks in advance. Best regards ___ 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] POL3 polarizable water model
I believe the manual says that only the shell-on-a-spring model is supported by GROMACS for polarization. As far as I can recall, the POL3 model uses atomic multipoles, so tough luck for you... 2008/3/25, Bo Zhou [EMAIL PROTECTED]: Dear Gromacs users, I wonder whether or not the POL3 polarizable water model (Caldwell JW, Kollman PA (1995) J Phys Chem 99: 6208-6219.) can be incorporated in gmx with amber03 force field. Thanks in advance. Best regards ___ 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] POL3 polarizable water model
Bo Zhou wrote: Dear Gromacs users, I wonder whether or not the POL3 polarizable water model (Caldwell JW, Kollman PA (1995) J Phys Chem 99: 6208-6219.) can be incorporated in gmx with amber03 force field. Thanks in advance. IIRC this is a point polarizability model. This is not implemented. The recent Drude/Shell models by us and the Charmm crew do work. Best regards ___ 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 van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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] combining the OPLS-AA forcefield with the Berger lipids
To wrap up combination of the OPLS-AA forcefield with the Berger lipids, I have posted a detailed description of the motivation, method, and testing. Much of the methods there will be used in a paper at some point in time so please do not copy the text directly for your own use. http://www.pomeslab.com/files/lipidCombinationRules.pdf ___ 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] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours
maria goranovic wrote: An update: Using a 4th order PME spline resulted in ~ 15 % increase in efficiency. Thank you, Carsten. As you can see in some of the original PME papers, tweaking the parameters can give about an order of magnitude variation in the approximation error for given computational cost, or similar variation in cost for a given error. pme_order = 6 works best on my hardware for error that I found acceptable. 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
[gmx-users] looking for help about the generating of opls forcefield
Hi all: How are you! I want to simulate the solution structure of a amino sugar gromacs, but I have no force field parameter about it. I have tried to obtain its forcefile parameter through prodrg and antechamber, and try my best to refine it. however, both calculated results with these forcefield parameter were unsatisfied. I hope someone can give me a hand if you have experience with generating ff parameter or you have interests. Thank you in advance! best regard ___ 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] query about itp file of sugar
SHREYA RAY CHAUDHURI wrote: I wnt to generate an itp file for carbihydrate which contains a glucose,a galactose and a neuraminidase.I want to know which force fied to use and the the linkages to use for the sugar.Please let me know the way by which I can make the itp file for the sugar.Eagerly waiting for a reply, Deciding which force field to use is something you must do. Read the literature and consider what you hope the simulation to achieve and make a decision that seems sound in the context of what other people have been doing. You may find that your choice of force field will drive your choice of simulation software. 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
Re: [gmx-users] Distance constrained energy minimization and MD
jayant james wrote: Hi all! The protein that I am trying to simulate has 3 chains. My aim is to apply harmonic constraints to certain parts of the protein and (based on FRET derived distances) I am attempting to incorporate distance constraint between certain amino acids of different chains during EM and MD. Constraints and restraints are different concepts in GROMACS. Look them up in the manual. _Harmonic Constraints_ I figured, that for the harmonic constraining the input is in the file posres_D.itp and I specify define = -DFLEXIBLE -DPOSRES in the em.mdp _Distance constraints _ I would also like to have amino acids contrained, not by a fixed distance but within a range(say 45-75 angstroms). How do I go about doing this? Check out distance restraints in the manual. 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
Re: [gmx-users] .itp file for polymer (Polystyrene)
Rohit wrote: Hi, I am trying to generate a polymer layer with 30 chains of 20 monomeric units using gromacs' genbox command. For that, I need to have .itp file for the single polymer chain (polystyrene). I have .itp file for styrene molecule, how can I make a .itp file for polymer chain using .itp file of styrene? I guess there must be some way to use parameters of styrene molecule to build up a .itp file for the polymer. I would appreciate If someone can help me with this. For a given n, you can build an n-styrene .top file with pdb2gmx. For this to work, you need a styrene .rtp file entry that defines head and tail atoms in a manner analogous to the peptide .rtp file entries, and probably you will also need to make .tdb entries to cap the chains. Read the relevant sections of chapter 5 and the wiki thoroughly, and experiment with this mechanism on peptides (where it already works) before trying to build the elements for your system. Once you have the .rtp and .tdb entries constructed, you give pdb2gmx a structure file containing the 20-styrene molecule, and it uses the residue numbering in that to infer the topology based on the .rtp entry. Then you edit the .top file by hand to become a 20-styrene .itp file. Then you can construct your 30-chain coordinate file somehow, #include the 20-styrene .itp file, construct a .top file by hand, and make sure its [ molecules ] entry has 30 styrene molecules. pdb2gmx might also be able to handle the 30 20-styrene coordinate file directly with the right command-line option, but I've never done it, so you're on your own there. 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
Re: [gmx-users] Error in equilibration
s lal badshah wrote: Dear Justin Mark, Hi! I made changes in my pr.mdp file but still the errors came.Please guide me. As you've read on the LINCS error page on the wiki, the errors are being caused by your starting structure being not-close-enough to something that makes physical sense, not anything in your .mdp file (although Justin's point about T-coupling was sound). 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
[gmx-users] OPLS-AA/L
Hi all, I am using gromacs 3.3.1 version.How can I generate OPLS-AA/L FF for POPC Thanks 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
[gmx-users] System
Dear Justin, Hi, I want to do MD simulation of cholera toxin A-subunit.I took PDB file and remove other complexes from the protein so it comes to 185 amino acid residues.Through Whatif server I added the missing atoms. I uses oplsaa force field.Added about 11700 water molecules, closed it in cubic box, added 5 sodium ions.Run the energy minimization but it didn't reached the full and output says:Converged to machine precision, but not to the requested precision.The EM value was in negative.Then I do the equilibration and the mentioned errors occured.My EM file is: title = cholera.mdp cpp= /usr/bin/cpp ; the c preprocessor include= -I/usr/share/gromacs/top define = -DFLEXIBLE constraints= none integrator = steep dt = 0.002 nsteps = 1 nstlist= 10 ns_type= grid rlist = 1.0 coulombtype= PME rcoulomb = 1.0 vdwtype= cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1es optimize_fft = yes ; ; Energy minimization stuff emtol = 1000.0 emstep = 0.01 -- Wile pr.mdp file istitle = pr.mdp cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 nsteps = 10 nstcomm = 1 nstxout = 250 nstvout = 1000 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e5 optimize_fft= yes ;Berendsen temperature coupling is on Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = protein non-protein ref_t = 298 298 ;Pressure coupling is on Pcoupl = berendsen tau_p = 20 20 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01.0 ;Generate velocities is on at 298 K gen_vel = yes gen_temp= 298 gen_seed= 173529 # Waiting for your reply. Regards, Lal badshah. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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] OPLS-AA/L
Check the archives. I posted a summary of one possible solution less than 8 hours ago. You will receive more assistance if you demonstrate that you are trying to help yourself. If you still don't find the answer that you are looking for then you need to be *way* more detailed in your question. Note that a lipid ff that can be used with OPLS-AA is an entirely different thing than an OPLS-AA lipid. If you truly want an opls-aa lipid then you are looking at months/years of difficult work and should start with the papers for parameterization of opls and follow their method. Chris. --original message -- Hi all, I am using gromacs 3.3.1 version.How can I generate OPLS-AA/L FF for POPC Thanks 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] .itp file for polymer (Polystyrene)
Thanks Mark for guiding me. Mark Abraham [EMAIL PROTECTED] wrote: Rohit wrote: Hi, I am trying to generate a polymer layer with 30 chains of 20 monomeric units using gromacs' genbox command. For that, I need to have .itp file for the single polymer chain (polystyrene). I have .itp file for styrene molecule, how can I make a .itp file for polymer chain using .itp file of styrene? I guess there must be some way to use parameters of styrene molecule to build up a .itp file for the polymer. I would appreciate If someone can help me with this. For a given n, you can build an n-styrene .top file with pdb2gmx. For this to work, you need a styrene .rtp file entry that defines head and tail atoms in a manner analogous to the peptide .rtp file entries, and probably you will also need to make .tdb entries to cap the chains. Read the relevant sections of chapter 5 and the wiki thoroughly, and experiment with this mechanism on peptides (where it already works) before trying to build the elements for your system. Once you have the .rtp and .tdb entries constructed, you give pdb2gmx a structure file containing the 20-styrene molecule, and it uses the residue numbering in that to infer the topology based on the .rtp entry. Then you edit the .top file by hand to become a 20-styrene .itp file. Then you can construct your 30-chain coordinate file somehow, #include the 20-styrene .itp file, construct a .top file by hand, and make sure its [ molecules ] entry has 30 styrene molecules. pdb2gmx might also be able to handle the 30 20-styrene coordinate file directly with the right command-line option, but I've never done it, so you're on your own there. 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 - Save all your chat conversations. Find them online.___ 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] Error in equilibration
Dear Justin, I try again by correcting the typo mistake I made, this time it gives the following type of out put; Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 224.227448 (between atoms 1932 and 1934) rms 4.182895 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 198200 49.70.1449 0.1615 0.1449 200201 90.10.1090 1.2643 0.1090 200202 46.80.1529 0.1690 0.1529 200211 41.20.1522 0.1686 0.1522 264265 70.90.1229 0.1349 0.1229 264266 47.20.1335 0.1443 0.1335 266267 66.80.1010 0.1148 0.1010 266268 70.10.1010 0.1010 0.1010 407408 32.70.1090 0.1091 0.1090 457458 90.00.1080 0.1195 0.1080 910912 51.30.1090 0.1088 0.1090 1001 1002 58.30.1090 0.1095 0.1090 1062 1065 90.00.1090 0.1098 0.1090 1249 1252 35.60.1509 0.1233 0.1510 1252 1253 38.80.1399 0.1381 0.1400 1252 1255 92.20.1399 0.5340 0.1400 1255 1256 89.80.1080 0.4882 0.1080 1255 1259 88.60.1400 1.2513 0.1400 1257 1261 84.50.1399 0.4295 0.1400 1259 1260 89.30.1080 1.0345 0.1080 1259 1261 90.20.1399 1.0302 0.1400 1261 1262 87.20.1364 0.3727 0.1364 1262 1263 89.30.0945 0.3040 0.0945 1926 1929 91.10.1529 0.1698 0.1529 1929 1930 91.10.1090 0.1885 0.1090 1929 1931 91.00.1090 0.2040 0.1090 1929 1932 90.20.1529 1.1270 0.1529 1932 1933 90.20.1090 1.0924 0.1090 1932 1934 90.00.1090 24.5498 0.1090 1932 1935 90.30.1463 1.1944 0.1463 1935 1936 92.00.1010 0.1697 0.1010 1935 1937 92.20.1340 0.1430 0.1340 2565 2566 90.00.1090 0.1235 0.1090 step 0Warning: 1-4 interaction between 196 and 201 at distance 1.104 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 10632.446289 (between atoms 1932 and 1933) rms 207.682693 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 170172 63.20.1335 0.1515 0.1335 172173 41.50.1449 0.1423 0.1449 172181 87.70.1449 0.2694 0.1449 173174 38.50.1090 0.1401 0.1090 173184 33.30.1522 0.1855 0.1522 175178 64.70.1529 0.2016 0.1529 178179 89.50.1090 0.1885 0.1090 178180 89.90.1090 1.3654 0.1090 178181 89.20.1529 0.2470 0.1529 181182 76.80.1090 0.2233 0.1090 181183 63.70.1090 0.2001 0.1090 200201 90.31.2643 0.2235 0.1090 200202 33.20.1690 0.1498 0.1529 200211 31.10.1686 0.1533 0.1522 202203 31.60.1045 0.1152 0.1090 202204 44.70.1033 0.1210 0.1090 202205 32.90.1481 0.1654 0.1529 211213 32.60.1352 0.1395 0.1335 261263 90.00.1083 0.4201 0.1090 266267 37.30.1148 0.1001 0.1010 266268 58.30.1010 0.1009 0.1010 455456 89.90.1082 0.2429 0.1080 457458 90.00.1195 0.2815 0.1080 910912 42.30.1088 0.1093 0.1090 1001 1002 44.50.1095 0.1091 0.1090 1062 1065 90.00.1098 0.1777 0.1090 1212 1222 102.30.1522 0.2192 0.1522 1222 1223 102.50.1229 0.2490 0.1229 1222 1224 92.30.1335 0.9308 0.1335 1224 1225 94.20.1010 0.8418 0.1010 1224 1226 91.40.1449 5.3237 0.1449 1226 1227 90.90.1090 4.9695 0.1090 1226 1228 92.00.1529 5.0058 0.1529 1226 1243 90.10.1523 121.0580 0.1522 1228 1229 92.30.1090 1.2347 0.1090 1228 1230 92.00.1090 1.2312 0.1090 1228 1231 90.90.1510 1.2383 0.1510 1231 1232 105.80.1400 0.2522 0.1400 1231 1234 105.00.1400 0.2524 0.1400 1243 1244 90.20.1230 121.2270 0.1229 1243 1245 89.90.1339 121.7164 0.1335 1245 1246 90.80.1013 7.4736 0.1010 1245 1247 91.20.1461 9.3242 0.1449 1247 1248 88.40.1101 3.5300 0.1090 1247 1249 87.90.1400 13.9017
Re: [gmx-users] Error in equilibration
s lal badshah wrote: Dear Justin, I try again by correcting the typo mistake I made, this time it gives the following type of out put; You still have a bad starting structure, even after your EM. Have a look at these atoms that are causing the actual error messages, since it might be a localised effect. Look for steric clashes, bonds that are too long, isolated water molecules, apparently non-formed bonds, etc. 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
