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<br> Thanks Justin. <br>Here is the quoted error:<br><hr size="2" width="100%"><br><i>processing topology...<br>Generated 2211 of the 2211 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 2211 of the 2211 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'Protein_chain_A'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>Excluding 1 bonded neighbours molecule type 'CL'<br>processing coordinates...<br>double-checking input for internal consistency...<br><br>ERROR 1 [file protein.top, line 9279]:<br> ERROR: One of the box lengths is smaller than twice the cut-off length.<br> Increase the box size or decrease rlist.<br><br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.5.3<br>Source code file: grompp.c, line: 1104<br><br>Fatal error:<br>There was 1 error in input file(s)<br>For more information and tips for troubleshooting, please check the GROMACS<br>website at http://www.gromacs.org/Documentation/Errors<br>-------------------------------------------------------<br><br>"Three Little Fonzies" (Pulp Fiction)</i><br><hr size="2" width="100%">and the mdp<br><hr size="2" width="100%"><i>; Lines starting with ';' ARE COMMENTS<br>; Everything following ';' is also comment<br><br>title = Energy Minimization ; Title of run<br><br>; The following line tell the program the standard locations where to find certain files<br>cpp = /usr/bin/cpp ; Preprocessor<br><br>; Define can be used to control processes<br>define = -DFLEXIBLE<br><br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>emtol = 1.0 ; Stop minimization when the maximum force < 1.0 kJ/mol<br>nsteps = 5000 ; Maximum number of (minimization) steps to perform<br>nstenergy = 1 ; Write energies to disk every nstenergy steps<br>energygrps = System ; Which energy group(s) to write to disk<br><br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>ns_type = simple ; Method to determine neighbor list (simple, grid)<br>coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.0 ; long range electrostatic cut-off<br>rvdw = 1.0 ; long range Van der Waals cut-off<br>constraints = none ; Bond types to replace by constraints<br>pbc = xyz ; Periodic Boundary Conditions (yes/no)</i><br><hr size="2" width="100%">Hope you can locate my error here!!<br><br><br><br>> Date: Wed, 17 Nov 2010 13:09:32 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Error on Box Length when adding ions        (gromacs        4.5.3/Charmm27/Tip3p)<br>> <br>> <br>> <br>> X Rules wrote:<br>> > I am having problems with grompp with my system.<br>> > <br>> > I am using Gromacs 4.5.3<br>> > FF = Charmm27 beta<br>> > WT = TIP3P (recommended and its claimed its not too different than <br>> > Charmms TIP3P)<br>> > <br>> > during minimization with pbc, I get the error about box length being <br>> > small if I add neutralizing ions (I do not get this error in just <br>> > water+protein system).<br>> > <br>> <br>> Providing your actual sequence of commands, .mdp file(s), and the actual <br>> (quoted) error message is the only way to diagnose what's going on.<br>> <br>> > Also I have tried increasing my box length upto a cube of 40 Angstroms <br>> > and still get the error ( I have a tiny 50 residue protein).<br>> > <br>> > IS IT A BUG or I am doing something wrong.<br>> > <br>> <br>> You're probably doing something wrong, but it's impossible to say what. Please <br>> provide more detail.<br>> <br>> -Justin<br>> <br>> > <br>> > I can add more information if needed.<br>> > <br>> > Thanks,<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>                                            </body>
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