[gmx-users] old and new versions of gromacs

Dear Gromacs Specialists I already worked with Gromacs-4.5.4. In the Gromacs site has been released new several versions. Has the old version (4.5.4) defects? Or are the new versions more complete? I want to continiue my simulations with 4.5.4, are there problems for it? I compared the manual

[gmx-users] old and new versions of gromacs

Dear Gromacs Specialists I already worked with Gromacs-4.5.4. In the Gromacs site has been released new several versions. Has the old version (4.5.4) defects? Or are the new versions more complete? I want to continiue my simulations with 4.5.4, are there problems for it? I compared the manual

Re: [gmx-users] GROMACS 4.6.3 Static Linking

Soneone said here that static versions are impossible for Cray... Dr. Vitaly V. Chaban On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner a.tur...@epcc.ed.ac.ukwrote: Hi I am having problems creating static versions of the GROMACS binaries for a Cray XE6 (www.hector.ac.uk). The build

[gmx-users] Comparing the simulation

Dear Friends, I did the Simulation study for self assembly of peptides . ( I used G96 53a6 FF ) In First Experiment, I put the two XX peptide far from each other 2.0 nm, and run the simulation. In the second experiment I put the two YY peptide seperated by 2.0 nm. and run

Re: [gmx-users] old and new versions of gromacs

On 7/20/13 2:58 AM, mohammad agha wrote: Dear Gromacs Specialists I already worked with Gromacs-4.5.4. In the Gromacs site has been released new several versions. Has the old version (4.5.4) defects? Or are the new versions more complete? I want to continiue my simulations with 4.5.4, are

Re: [gmx-users] Comparing the simulation

On 7/20/13 5:27 AM, rama david wrote: Dear Friends, I did the Simulation study for self assembly of peptides . ( I used G96 53a6 FF ) In First Experiment, I put the two XX peptide far from each other 2.0 nm, and run the simulation. In the second experiment I put the

[gmx-users] atomtypes in .n2t

Dear users To generate a topology file for an arbitrary molecule, I used g_x2top program. I added following lines to atomname2type.n2t: .. .. C opls_145B 0.080627 12.0110 3 C 0.1395 C 0.1395 C 0.149 C opls_145B 0.091698 12.0110 3 C 0.149 C 0.1395 C 0.1395 .. But,

[gmx-users] old and new versions of gromacs

Dear Justin, Thank you very much from your response. Best Regards Sara From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, July 20, 2013 3:47 PM Subject: Re:

[gmx-users] Compilation problem with Gromacs 4.5.7 (autoconf only)

Hello, I am not sure whether this is a known problem, but it seems gromacs-4.5.7 compilation using autoconf tool is still broken (at least for me). The ./configure step completes without any error. But make fails with the following error regarding not finding certain version of aclocal and

[gmx-users] Setting attractive part (C6 parameter) zero in non-bonded parameters

Hello, Following the Section 5.3.2 of the manual, I have tried to set the C6 term of the non-bonded (Lennard-Jones) interaction to zero as follows: When sigma and epsilon need to be supplied (rules 2 and 3), it would seem it is impossible to have a non-zero C12 combined with a zero C6

Re: [gmx-users] Comparing the simulation

Dear Justin, Thank you for your Prompt Reply. I run a at least 4-5 run of each peptide. The result are like the xx peptide form beta structure early than yy peptide in each run. I just used the different tau_P ( relaxation time ) for NPT and MD production run. XX tau_p = 2 YY

[gmx-users] Question on Hessian and forces not being preserved on restart with Hessian calculation?

When I minimize a structure, I can get down to the force max being 0.01 Low-Memory BFGS Minimizer converged to Fmax 0.01 in 6839 steps Potential Energy = -5.12340607768673e+03 Maximum force = 6.68907856457542e-03 on atom 3029 Norm of force = 2.19978176343026e-03 kJ/nm. However, when

[gmx-users] Re: Question on Hessian and forces not being preserved on restart with Hessian calculation?

To follow up -- if I try to minimize again using -t, I get the same low forces as in the minimization in the previous step. So it appears to be something with what do_nm is doing, not with errors in the output structure. On Sat, Jul 20, 2013 at 9:37 AM, Michael Shirts mrshi...@gmail.com wrote:

[gmx-users] Re: Question on Hessian and forces not being preserved on restart with Hessian calculation?

Problem partly addressed. If I run normal modes in -nt 1, then I get the same force as after the minimization. I'll file a redmine. On Sat, Jul 20, 2013 at 9:43 AM, Michael Shirts mrshi...@gmail.com wrote: To follow up -- if I try to minimize again using -t, I get the same low forces as in

Re: [gmx-users] atomtypes in .n2t

On 7/20/13 7:35 AM, afsaneh maleki wrote: Dear users To generate a topology file for an arbitrary molecule, I used g_x2top program. I added following lines to atomname2type.n2t: .. .. C opls_145B 0.080627 12.0110 3 C 0.1395 C 0.1395 C 0.149 C opls_145B 0.091698 12.0110

Re: [gmx-users] Comparing the simulation

On 7/20/13 9:12 AM, rama david wrote: Dear Justin, Thank you for your Prompt Reply. I run a at least 4-5 run of each peptide. The result are like the xx peptide form beta structure early than yy peptide in each run. I just used the different tau_P ( relaxation time ) for NPT and MD

Re: [gmx-users] velocity-verlet giving nans

On Fri, Jun 7, 2013 at 11:52 AM, Mark Abraham mark.j.abra...@gmail.com wrote: If you want to suggest fixing any possible problem, please file an issue at redmine.gromacs.org There is already a report in redmine with a suggestion on how to deal with NaNs: http://redmine.gromacs.org/issues/941

[gmx-users] mdrun error

Dear Users, when trying to run the following command: mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb I have received the error below. Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) Starting 2 threads ---