Re: [gmx-users] ffamber03 top file problem
Check the topology section in the gromacs manual. You'll find the format you should use for bonds, angles etc.On 15-02-11, gromacs564 gromacs...@126.com wrote:Dear All: I want to obtain a top file for protein with ffamber03 force field,and correct some bonds and angles parameter. I added a new atom type HD(D2O) in ffamber03 [ atomtypes ], so I added some HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of the program indicate:---Program grompp_m, VERSION 4.5.1Source code file: toppush.c, line: 1631Fatal error:Incorrect number of parameters - found 1, expected 2 or 4 for Bond.For more information and tips for troubleshooting, please check the GROM···I added some bonds and angles parameters like this:··; residue 44 ASN rtp ASN q 0.0 664 N 44 ASN N 664 -0.430106 14.01 ; qtot 4.57 665 HD 44 ASN HD 665 0.250466 2.016 ; qtot 4.824 666 CT 44 ASN CA 666 0.044609 12.01 ; qtot 4.869···[ bonds ]; ai aj funct c0 c1 c2 c3··· 676 678 1 678 679 1 0.10115 678 680 1 680 681 1 ···[ angles ]; ai aj ak funct c0 c1 c2 c3 648 650 652 1 651 650 652 1 115.149 650 652 653 1 650 652 654 1 Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] lipid order parameter
On Wed, 2 Aug 2006 19:58:21 -0700 (PDT) priyanka srivastava [EMAIL PROTECTED] wrote: This reference is the one which reports sn2 but I am looking for sn1 as well. :-( Pri... A lot of simulations of DMPC have been published and comparison with experimental order parameters for the tails was certainly included. Did you look for this papers ? XAvier [EMAIL PROTECTED] wrote: Dear Gromacs users, I am looking for individual experimental (NMR) order parameter values for sn1 and sn2 chains at physiological temperature for DMPC in order to carry out the analysis of my trajectories and compare the results. I have got the values for sn-2 chain but unable to get it for sn1chain of DMPC. Though this question is not directly related to gromacs but this is the place where many people deal with lipids and its parameters. Please put it up on the forum in case anybody has the reference or the values. I would be really thankful, waiting for the response, Pri... Hi, maybe you will find it in DOULIEZ, J.P., LÉONARD, A. DUFOURC, E.J. Restatement of order parameters in biomembranes: calculation of C-C bond order parameters from CD quadrupolar splittings. Biophys. J, v. 68, p. 1727-1739. 1995 Cheers. Pedro. This message was sent using IMP, the Internet Messaging Program. ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 - Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] g_hbond account dieletric medium ?
I have shown hydrogen bond formation between guanidino side chain of Arginine and carboxylate in sidechain of Aspartate out my simulation result using g_hbond. Now I see those two residues are well exposed in solvent. Since g_hbond compute hydrogen bonds based on only distance and angles, how I can prove that hydrogen bonds formed between those groups are by overcoming the dielectric medium of waters? What do you mean exactly by overcoming the dielectric medium of water ? XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Gramicidin A
Hello everyone, I am interested in simulating gramicidin A channel in DPPC membrane. I noticed there were few papers already published on this particularly Biophysics Journal Vol. 82 June 2002, by de Groot, Tieleman, Pohl and Grubmuller. Does anyone has the structure along with the topology files so that I dont have to duplicate things. What about contacting the authors !! XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] pdb2gmx residue error
I am trying to do a simple NaCl solvation and MD run using GROMACS. I have 4 atoms in my (.xyz) file for the 2 Na's and 2 Cl's. I convert the (.xyz) to (.pdb) using babel. Afterwards, I try to generate the topology file using pdb2gmx program and it generates an error. I am using the 43a1 force field. FATAL ERROR: Residue LIG not found in residue topology database. What does LIG represent in your pdb file ?? The best way would probably be to first construct a box of water (editconf, genbox) and then put ions inside, manually by removing water molecules or using genion ! XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Fe(II) at active site
During the simulation of protein with Fe (II) ligating with 2 His and 1 Asp residues at active site, I set every thing right including Kb value but failed to deprotonate NE2 atoms of 2 His residues ligating that Fe(II). What do you mean by failed ? This should not be a problem. You can choose the protonation state of a his ... check the ffXXX.rtp file. After 2ns simulation run, the average pdb structure shows that the flip of His ring out from Fe (II), but the Asp-oxygen moved much closer to Fe (II) than its original position. If I compute RMSF for Fe (II), showing value of 0 through out the simulation run. The RMSF 0 indicates Fe (II) originally retained in its position, 0 fluctuations at all !!! You fixed its position or something ? That does not seems right !! but the ligating His flipped and Asp as a single residue held the Fe (II) at its original position. So now please tell me whether this simulation is valid? The simulation that you discribe does not seem to be a good representation of your system ... XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Fe(II) at active site
Raja, Thanks for your opinion. This is my maiden attempt to simulate a protein so the reason for the mistake. If possible could you please refer me some paper, which describe the simulation of a system, contains Fe (II) at its active site. I tried my best, but could not find a one. I am affraid that there are not much of this type of study. Ions are a big issue in MD simulations ! I personaly can not remember any with Fe-II !! May be other users could point you to such studies. Sorry, XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Fe(II) at active site
One idea could be to look for simulations of proteins that are known to bind Fe !!! XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Fe(II) at active site
Well, you made a point of Ions are big issue in MD simulations. Could you please hint me what possible issues, so I can search relavent to those keywords. The main issue is the charge transfert which is not possible to model with a basic MM force fields. Then simulating a protein with an ions becomes an issue ! One reasonable think to do is to define convalent bonds between the ions and the atoms interacting with it in the protein. You won't see any change in the ion coordination ... that should apply to your system. Look the email list this issue was discussed many times. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] does gromos force field can explain pi-pi interaction
My simulation shows that the aromatic ring of ligand forms stacking pi-pi interaction with the side chain of Phe of receptor during MD simulation. One reviewer of my manuscript questions that such pi-pi interaction can not accurately accounted for by the employed force field. I do not know how to answer this question, any idea is highly appreciated! None of the MM force field can reproduce pi-pi interactions for the simple reason that the force field does not describe electrons explicitly !! That is the case for most of the interactions involving electrons !! The same for H-bonds. At the time of FF development their were a big problem !! Not transfert of electrons in MM !! Basically a FF sucks when a chemist looks at it !! On the other hand the MM-FF have been parametrized to reproduce average properties of small compounds (see the GROMOS FF description) and several type of funny interactions can be observed. In the GROMOS FF the C in the rings in PHE and TYR have partial charges to reproduce the delocalization of the electrons ... as a comparison the C of the LYS side chain do not have any partial charges !! What you see is not a pi-pi stacking interaction but an interaction between two rings that could be assimilated to a pi-pi interaction although you do not have explicit description of electrons or polarization. There different ways to say things !! Saying you have pi-pi stacking is definitely too much. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Position restraints for a part of the protein
I used 'genpr' to generate the 'posre.itp' file as I did many other times to restrain the entire protein leaving the solvent free. Once I run 'grompp' I get the following message: Fatal error: [ file 1_Cter.top, line 7895 ]: Atom index (152) in position_restraints out of bounds (1-3) where atom 152 is the first atom in the protein that I want to restraint. It looks like the molecule you try to apply the position restrain to is a solvent molecules (3 atoms). You should check that grompp takes the right posres.itp for the molecule. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Converting pdb to tpr
On Mon, 24 Jul 2006 09:50:09 +0100 Samantha Kaye [EMAIL PROTECTED] wrote: Hi, I found a thread on the gmx-users mailing list that said using pdb2gmx will allow you to convert a pdb file to a tpr file. However, when I use pdb2gmx -h I cannot see which option will allow me to do this. Can someone tell me please? You might want to go through the gmx tutorial. All the steps to get from a pdb to tpr file and then an MD simulation are introduced. In brief the function pdb2gmx is to generate a topology file (topol.top) of your system, e.g. protein, then you would solvate your system, and finally use grompp together with a coordinate file, a topology and a file containing the way you want to simulate (mdp file) ... then you'll run. pdb2gmx does not generate a tpr file !! XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Converting pdb to tpr
That's what I thought. I wanted to use g_hbond on frames of a trajectory that I have docked a ligand into to extract the contacts made. However, my initial tpr file doesn't have the ligand in as it was never there in the initial simulation. I'll just have to think of another way to look at the h-bonds. look at ligplot that would be good to do this ! XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Re: editconf -d
On Thu, 20 Jul 2006 10:24:25 +0200 (CEST) Isabella Daidone [EMAIL PROTECTED] wrote: Hi, this is what is written in one of the options in editconf: -[no]c bool no Center molecule in box (implied by -box and -d). Now you mention it ! did you try a two step process: 1) center (-c), 2) the edges (-d). Could be the combination that goes wrong ! Moreover, in the mailing list you can find discussion about this topic with version 3.2 and David said it was a bug (that -d -c did not really center). So they should comment ! I have no idea. Sorry XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] setting up a random system
On Mon, 10 Jul 2006 15:13:19 +1200 erwin berthier [EMAIL PROTECTED] wrote: Hello Mark and Jay, Thanks for your advice. I see that if I start a system quite less dense and let it equilibrate during the run it avoids a lot of problems. If I don't do that even the energy minimisation process fails. But that seems to work now. I thought about removing some particles by hand but is there a program that redistributes atom numbers (somehow I don't have the motivation for a 10 atom system)... It would be a pretty easy script to write though, but if the tool already exists... editconf -f toto.gro -o toto-cleaned.gro would give the right number in the output. Don;t forget to change the total atom number at the begining of the file. About that pressure scaling problem what is the importance of tau_p? What does it mean if I change it from 1 to 100 for example? Cheers, Erwin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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] tpbconv
I was running a parallel MD simulation, the program stopped (no more output data) in the middle without any error message in the log file. When I use command top to check the process, the output message showed the program was still running, but no more output data. Therefore I killed the job, and tried to continue it by tpbconv -f -e -o continue I didn't specify the extension time because I just want to finish the rest of the simulation. The following message is what I got from tpbconv: You should check the content of your trajectory, how long was it suposed to run ? Don't feel embarased to use the until option ... it works fine. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] How do Charge Groups work?
I had a system where I have no charges in it, but I do have Lennard-Jones non-bonded interactions. I've noticed that I get different values for the Lennard-jones interaction energy differs depending how I split the system up into charge groups (as the charge group concept is kinda abitrary in a system with no charges), this can not be right surely? As I understood it the charge groups were used to help compile the neighbour lists, but what I want is all the atoms within my cut-off radius to be in my pair-list (for that atom). Is there an option to ignore the charge groups? I find I get bigger Lennard-Jones interactions if I put my whole system into a charge group that if I split it up, but I need to split it up for my larger systems. Is there a way to increase the maximum number of charge groups? And is this a good idea? You should check the manual for the option allowing a atom base cutoff, I am not sure it actually exist. A crude way to fix it would be to define each atom as a seprate charge group. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] [Fwd: DNA separation]
On Sun, 21 May 2006 23:09:15 +0200 Beniamino Sciacca [EMAIL PROTECTED] wrote: Dear community, I've a problem during the MD of a double strand molecule of DNA. I worked with heavy H and virtual site. I minimized in vacuum, then i solvated and minimezed. Later I've heated (simulated annealing) for 50 ps. Then I simulated 1200 ps of MD. There has not been any crash. Viewing RMSD, in 4 point there is a peak. Viewing, with VMD, the dinamic in the same steps the molecule is separated in 2 molecule single strand; the next step the molecule return in double strand configuration and the dinamic continue without any problem. It seems that you are experiencing molecules jumping over the periodic box !! You have the filter your trajectory using trjconv and play wioth the options -pbc, may be nojump, to view your system as a whole. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] How many ps needs a simulation?
On Wed, 10 May 2006 19:29:26 -0700 (PDT) jahanshah ashkani [EMAIL PROTECTED] wrote: Thanks, In fact I have a sequence with 1277 residue. It is stable even in 50ps. But when I continue to simulation my pc is restarted in 4 steps, automaticly. I should say that this step needs about 100 h time. 50 ps for a protein of 1277 residue is probably equivalent to the first minute of a marathon. The system size you chose can be considered enormous ! Anyway as M and W already said, the simulation length that would give you a reasonable answer depends entirely on what question you want to answer and the quality of the answer you want. From a 50ps simulation you have absolutely no answer at all !! Good luck XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] conformation search
On Sat, 29 Apr 2006 08:13:33 +0800 Rongliang Wu [EMAIL PROTECTED] wrote: Hello, gmx-users， is it possible to do conformation searches using gromacs? and how? What do you mean by conformation searches ? XAvier Regards Thanks Rongliang Wu [EMAIL PROTECTED] 2006-04-29 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] How to make the missing atom by PRODRG
On Fri, 28 Apr 2006 20:34:17 -0700 raja [EMAIL PROTECTED] wrote: Hi GMXIONS, A hydrogen atom attached to carboxylate oxygen is missing in output gro file for a ligand produced by DUNDEE PRODRG server. If you mean that you want to portonate (neutralize) a corboxyl group ... you can do this through pdb2gmx using the -glu flag that would give you the choice of protonation state for all gl in your system. XAvier How to add that hydrogen manually , Is there way to do that in any of available software ? With thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Relatively orient two molecules: rotation and/ortranslation
On Sat, 29 Apr 2006 01:56:34 -0400 Tandia, Adama [EMAIL PROTECTED] wrote: Dear Gromacs Users, I'm looking for an easy way to relatively orient two large molecules (many rings with long CnH2n+1 tails): keep one fixed and translate and/or rotate the second one with respect to a given direction. The idea behind would be to fill up then the box with a solvent and run a position restrained MD. You can wrie a simple script or programm that would translate/rotate one of your molecule ... or use a visualization programmm (Rasmol, VMD) and tell to treanslate, rotate according to your need. This is trivial opration of any visaulization program. XAvier Does anyone have an idea of a freeware to do that? Regards, Adama Adama Tandia Corning INC Corning, NY USA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 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] questions about implicit solvent simulation
Dear Linchen, As Mark already told you there is no implicit solvent implementation in GROMACS ! The reaction field and generalized reaction field options are corrections to the long range electrostatic interactions. If you want to use an different dielectric cosntant than one you have to specify it in the mdp file with the keywork epsilon. Check out the manual for this, it must be indicated. I want to do a implicit solvent MD simulation. I wonder whether gromacs can fullfill the goal, if so, which option should I choose for electrostatics, reaction field or generalized reaction field? And what rcoulomb value is appropriate? if not, could I do a energy minimization for my protein in an enviroment of dielectric constant other than 1? Thanks a lot for your attention:) XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] LINCS Warning with MDRUN - Segmentation Fault
On Mon, 17 Apr 2006 00:07:29 -0700 Gaurav Chopra [EMAIL PROTECTED] wrote: Hi I am getting the following error with mdrun. I have done a few things but the system complains of 1-4 interactions and gives LINCS warning if the constraints are not turned off in the mdp file. I also changed the fudgeQQ = 1.0 (instead of 0.5) in ffoplsaa.itp and then did mdrun but I get 1-4 interaction table size error and then LINCS warning. The output of mdrun for one of these peptides is as follows. I am working on normal mode decoys of each peptide and many of the decoys have no problems with mdrun but some gives this error and Segmentation Fault. Please advice. The lincs warnning are on water molecules isn't it ??? XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Energy Minimization Problem
On Mon, 17 Apr 2006 08:21:35 -0400 (EDT) Robson P. S. Peguin [EMAIL PROTECTED] wrote: Hi everybody, I'm trying to simulate an interfacial system using Gromacs. My simulation box has water in one side and hydrofluorocarbon in the other side. This system was successfully tested using DL-POLY simulation package previously. Also, the box containing pure hydrofluorocarbon worked fine using Gromacs. However, when I try an energy minimization simulation with the interfacial system, after a couple of steps (~400), the geometry of the hydrofluorocarbon changes. I mean, the molecules begin to lose bonds or atoms. It didn't collapse the box yet, but I can see from a visualization package that the molecules are distorted. I tried to decrease the timestep unsuccessfully. If you have any suggestions, I'll be happy to know them. You should check your topology: bond definition from what you describe lokks necessary. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Membrane error
On Tue, 4 Apr 2006 00:17:25 -0500 Kushal Seth [EMAIL PROTECTED] wrote: HI all ! I am gettting this error while doing my simulation... for the bilayers Back Off! I just backed up emout-nowater.mdp to ./#emout-nowater.mdp.1# checking input for internal consistency... ...ling /usr/bin/cpp : No such file or directory cpp exit code: 32512 -I/usr/local/gromacs/share/gromacs/top mytop-nowater1.top gromppdriwHo' ' command is defined in the .mdp file processing topology... processing coordinates... --- Program grompp, VERSION 3.3 Source code file: grompp.c, line: 427 Fatal error: number of coordinates in coordinate file (binaryCR-Ochol-box-largeZ.pdb, 10280) does not match topology (mytop-nowater1.top, 0) there is definitely a problem in the definition of your system in the mytop-nowater1.top ... the systm does not see any atom in there. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] How many boundary conditions in GMX?
Maybe, this is a stupid question, but I really have no concepts about other kinds of boundary conditions except for pbc. Anybody know how many or which boundary condition is used in GMX except for pbc, and how to set the parameters in the input files? Because I wanna make a comparison with the results under pbc. You can find some the explaination of the type of pbc and the way use them within gmx in the manual and certainly extended explainations in any book introducing MD simulations. This can not easily explained by email. Best XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Re: How to generate itp files of small moleclues for gromos96 force field
On Tue, 21 Mar 2006 10:45:06 +0800 Shulin Zhuang [EMAIL PROTECTED] wrote: By the way, for the optimal setup of molecluar dynamics, there are some difference for gromacs and gromos, such as in the mdp file, GROMOS 96 force field uses nstlist = 5 and rvdw = 1.4. Can anyone give me a standard mdp file to do MD simulation with gromacs package using gromos96 force field? gromacs has to be used is the exact same way as defined by gromos. that is nstlist=5 and twin cut-off 8-14Ang. Don't forget the Reactio-field for the Electrostatic. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Not enough ref_t and tau_t values
On Wed, 15 Mar 2006 17:21:52 -0600 Ashutosh Jogalekar [EMAIL PROTECTED] wrote: I know this question has been discussed a number of times on the list, but almost everytime it has been discussed in reference to the index file. I am getting this error during grompp for the position restrained MD even though I am not using any index file. The only groups I have are solvent and protein and accordingly, there are two columns for these two in the tau_t and ref_t fields in the pr.mdp file: tau_t= 0.1 0.1 tc_grps= protein sol ref_t=300 300 my command is: grompp -f pr.mdp -c test_b4pr.gro -p test.top -o test_em.tpr In spite of this, the error is showing up again and again. The top file also has a row only for protein and solvent. If all the atoms of your protein or solvent are not included in the indexes defined by default (protein sol) I think grompp find them out of any index and then looks for more tau_t and ref_t ... I would check the topology of your system. It might be uncorrect. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
