[gmx-users] A small gift for you.
Hey Discussion,Click below or paste this into your browser:http://youmint.com/network-bhanu_seniya Make money every time Advertisers send you email or SMS.You have received this email because two of your friends have invited you. If you do not wish to receive any further notiications, Decline . Copyright 2007-2008 YouMint Media (P) Ltd. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] A small gift for you.
Hey Discussion,Click below or paste this into your browser:http://youmint.com/network-bhanu_seniya Make money every time Advertisers send you email or SMS.You have received this email because two of your friends have invited you. If you do not wish to receive any further notiications, Decline . Copyright 2007-2008 YouMint Media (P) Ltd. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] (no subject)
hello sir.. i have a problem in running pdb2gmx command fatal error is : atom c1 in residue na+ 369 not found in rtp entry with 1 atom while soting atoms -- Er. Chandrabhan Seniya Lecturer, Deptt. of Biotechnology, MITS Gwalior (M.P.) INDIA Mob : 09755213002 ___ 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] position restraints
what is yr real prob tell me? On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting chandrabhan seniya <[EMAIL PROTECTED]>: > > > no prob you wait for some time it will write topology file and the > proceed > > further.. > > I think that a lipid molecule trying to tear itself apart at step 0 would > fall > under the category of a "problem," and it will not disappear on it's own > if we > conveniently ignore it... > > > > > On Thu, Apr 24, 2008 at 5:04 PM, <[EMAIL PROTECTED]> wrote: > > > > > Hi, > > > > > > The full mdrun output when the simulation blows up is: > > > > > > Step 0, time 0 (ps) LINCS WARNING > > > relative constraint deviation after LINCS: > > > max inf (between atoms 6 and 7) rms inf > > > bonds that rotated more than 30 degrees: > > > . > > > . > > > . > > > Warning: 1-4 interaction between 1 and 6 at distance > > > 324490777485109120.000 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 > > > > > > Thanks Gadi > > > > > > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > > > > > > > > > > Did your minimization converge to a nice, negative potential energy? > > > > Also, what > > > > is the full mdrun output when the simulation blows up? You've > quoted > > > > the last > > > > bit, but it would be more informative to see the whole output, or at > > > > least a > > > > description of it (i.e., LINCS warnings). > > > > > > > > -Justin > > > > > > > > Quoting [EMAIL PROTECTED]: > > > > > > > > > > > > > Hi, > > > > > > > > > > I tried using no temperature coupling and no constraints, that did > not > > > > > help. > > > > > If I run the simulation without the position restraints it works > OK. > > > > > Could there by something wrong with the posre file (I'll attach it > at > > > > > the end of the email). > > > > > I want one of the atoms in the lipid to stay in one place and the > rest > > > > > to wiggle around it. Is there any other way to do that which is > not > > > > > position restraints. > > > > > > > > > > Thanks Gadi > > > > > > > > > > > > > > > [ position_restraints ] > > > > > ; atom type fx fy fz > > > > > 1 1 0 0 0 > > > > > 2 1 0 0 0 > > > > > 3 1 0 0 0 > > > > > 4 1 0 0 0 > > > > > 5 1 0 0 0 > > > > > 6 1 0 0 0 > > > > > 7 1 0 0 0 > > > > > 8 1 1000.0 1000.0 1000.0 > > > > > 9 1 0 0 0 > > > > > 10 1 0 0 0 > > > > > 11 1 0 0 0 > > > > > 12 1 0 0 0 > > > > > 13 1 0 0 0 > > > > > 14 1 0 0 0 > > > > > 15 1 0 0 0 > > > > > 16 1 0 0 0 > > > > > 17 1 0 0 0 > > > > > 18 1 0 0 0 > > > > > 19 1 0 0 0 > > > > > 20 1 0 0 0 > > > > > 21 1 0 0 0 > > > > > 22 1 0 0 0 > > > > > 23 1 0 0 0 > > > > > 24 1 0 0 0 > > > > > 25 1 0 0 0 > > > > > 26 1 0 0 0 > > > > > 27 1 0 0 0 > > > > > 28 1 0 0 0 > > > > > 29 1 0 0 0 > > > > > 30 1 0 0 0 > > > > > 31 1 0 0 0 > > > > > 32 1 0 0 0 > > > > > 33 1 0 0 0 > > > > > 34 1 0 0 0 > > > > > 35 1 0 0 0 > > > > > 36 1 0 0 0 > > > > > 37 1 0 0 0 > > > > > 38 1 0 0 0 > > > > > 39 1 0 0 0 > > > > > 40 1 0 0 0 > > > > > 41 1 0 0 0 >
Re: [gmx-users] position restraints
no prob you wait for some time it will write topology file and the proceed further.. On Thu, Apr 24, 2008 at 5:04 PM, <[EMAIL PROTECTED]> wrote: > Hi, > > The full mdrun output when the simulation blows up is: > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max inf (between atoms 6 and 7) rms inf > bonds that rotated more than 30 degrees: > . > . > . > Warning: 1-4 interaction between 1 and 6 at distance > 324490777485109120.000 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 > > Thanks Gadi > > Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > > > > Did your minimization converge to a nice, negative potential energy? > > Also, what > > is the full mdrun output when the simulation blows up? You've quoted > > the last > > bit, but it would be more informative to see the whole output, or at > > least a > > description of it (i.e., LINCS warnings). > > > > -Justin > > > > Quoting [EMAIL PROTECTED]: > > > > > > > Hi, > > > > > > I tried using no temperature coupling and no constraints, that did not > > > help. > > > If I run the simulation without the position restraints it works OK. > > > Could there by something wrong with the posre file (I'll attach it at > > > the end of the email). > > > I want one of the atoms in the lipid to stay in one place and the rest > > > to wiggle around it. Is there any other way to do that which is not > > > position restraints. > > > > > > Thanks Gadi > > > > > > > > > [ position_restraints ] > > > ; atom type fx fy fz > > > 1 1 0 0 0 > > > 2 1 0 0 0 > > > 3 1 0 0 0 > > > 4 1 0 0 0 > > > 5 1 0 0 0 > > > 6 1 0 0 0 > > > 7 1 0 0 0 > > > 8 1 1000.0 1000.0 1000.0 > > > 9 1 0 0 0 > > > 10 1 0 0 0 > > > 11 1 0 0 0 > > > 12 1 0 0 0 > > > 13 1 0 0 0 > > > 14 1 0 0 0 > > > 15 1 0 0 0 > > > 16 1 0 0 0 > > > 17 1 0 0 0 > > > 18 1 0 0 0 > > > 19 1 0 0 0 > > > 20 1 0 0 0 > > > 21 1 0 0 0 > > > 22 1 0 0 0 > > > 23 1 0 0 0 > > > 24 1 0 0 0 > > > 25 1 0 0 0 > > > 26 1 0 0 0 > > > 27 1 0 0 0 > > > 28 1 0 0 0 > > > 29 1 0 0 0 > > > 30 1 0 0 0 > > > 31 1 0 0 0 > > > 32 1 0 0 0 > > > 33 1 0 0 0 > > > 34 1 0 0 0 > > > 35 1 0 0 0 > > > 36 1 0 0 0 > > > 37 1 0 0 0 > > > 38 1 0 0 0 > > > 39 1 0 0 0 > > > 40 1 0 0 0 > > > 41 1 0 0 0 > > > 42 1 0 0 0 > > > 43 1 0 0 0 > > > 44 1 0 0 0 > > > 45 1 0 0 0 > > > 46 1 0 0 0 > > > 47 1 0 0 0 > > > 48 1 0 0 0 > > > 49 1 0 0 0 > > > 50 1 0 0 0 > > > > > > Quoting Mark Abraham <[EMAIL PROTECTED]>: > > > > > > > [EMAIL PROTECTED] wrote: > > > > > > > > Please generate replies to the mailing list sensibly. It's very hard > > > to > > > > work out who you are quoting where in this email. It'd be easy just > > > to > > > > ignore it, and that's the last thing you should want. > > > > > > > >> Hello, > > > >> > > > >> I'm trying to run a simulation with one lipid molecule in a fixed > > > >> simulation box without pbc. > > > >> I set position restraints on one of the atoms and I seem to keep on > > > >> getting the following error: > > > > > > > > Why do you want MD of a single lipid and a position restraint on one > > > > atom? If you just want to see a lipid wiggle around, then don't > > > create > > > > more numerical complexity. > > > > > > > >> The lipid is DPPC.The .itp file I got from a coworker that used it > > > >> before for membrane MD simulations. > > > >> To minimize the system I used steepest descent with the following > > > >> parameters: > > > > > > > > Well if your grompp and mdrun completed successfully and without > > > > warnings then you've probably got an OK topology and structure. > > > > > > > > The combination of all bond constraints, a single lipid in vacuo, > > > > temperature coupling and a single position restraint sounds like a > > > > recipe for a numerical disaster, i.e. blowing up. Try with fewer of > > > > those things applied, or get a more physically-reasonable system, > > > like > > > > a whole membrane. > > > > > > > > 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
