Re: [gmx-users] Fwd: Broken chain / fragmentation

On 5/27/17 9:42 AM, Tasneem Kausar wrote: Try -pbc whole And for a more complete explanation: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin On 27 May 2017 18:09, "Biplab Ghosh" wrote: Dear Gromacs users, My Gromacs

Re: [gmx-users] Grompp error for graphene modeling

On 5/27/17 3:33 AM, ‪Mohammad Roostaie‬ ‪ wrote: Hi All, I modeled graphene in a box of water with a peptide in the center of the box. I modified the OPLS-AA force field by adding the parameters from this link to the modified force field: http://chembytes.wikidot.com/grocnt. But, when I want

Re: [gmx-users] RMSF per residue

On 5/26/17 1:20 PM, Mohsen Ramezanpour wrote: Hi Justin, Here is what I understand. I would like to know if I understood correctly. Given a selection, which has all the heavy atoms (5 atoms) in the side chain of one specific residue (say Lysine), I want to have only "one value" for the

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

On 5/27/17 2:44 PM, Erik Marklund wrote: Hi Mark, Thinking out loud: “Non-Hbonding pairs within 3.5 Å”. I think it should be more explicit, and exactly what we always tell people: -num: number of hydrogen bonds as a function of time. The second column contains the number of atom pairs

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

Hi Mark, Thinking out loud: “Non-Hbonding pairs within 3.5 Å”. Kind regards, Erik > On 27 May 2017, at 17:56, Mark Abraham wrote: > > Hi, > > So what should we document in the help text as the meaning, so we don't > keep having emails about this? > > Mark > > On

[gmx-users] NMA Hessian Sub-matrix

Dear Gmx-User, I would like to know if It is possible to calculate just a submatrix of the Hessian matrix during the normal mode analisys?? I have a very large system (protein +membrane + water). I minimized the entire system but I would like to calculate the part of the Hessian matrix

Re: [gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

Dear All, I would like to come back to this discussion with following question. What if I need to use CHARMM22 FF for protein in water box + counterions and I have a computational package that does not support Verlet algorithm for neighbour search but link cells (index cells) approach instead? To

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

Hi, So what should we document in the help text as the meaning, so we don't keep having emails about this? Mark On Sat, May 27, 2017 at 4:36 PM Erik Marklund wrote: > > > On 26 May 2017, at 22:12, David van der Spoel

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

On 26 May 2017, at 22:12, David van der Spoel > wrote: On 26/05/17 22:05, Erik Marklund wrote: “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is why they are sometimes fewer than the hbonds. Therefore I would assume

Re: [gmx-users] Fwd: Broken chain / fragmentation

Try -pbc whole On 27 May 2017 18:09, "Biplab Ghosh" wrote: > Dear Gromacs users, > > My Gromacs simulation on a protein terminated without any error and major > warning. However, when I see the conformations, I found them broken. > > For trajectory conversion, I have

[gmx-users] Fwd: Broken chain / fragmentation

Dear Gromacs users, My Gromacs simulation on a protein terminated without any error and major warning. However, when I see the conformations, I found them broken. For trajectory conversion, I have used the following commands: gmx trjconv -s protein-md.tpr -f protein-md.xtc -center -pbc nojump

[gmx-users] Grompp error for graphene modeling

Hi All, I modeled graphene in a box of water with a peptide in the center of the box. I modified the OPLS-AA force field by adding the parameters from this link to the modified force field: http://chembytes.wikidot.com/grocnt. But, when I want to add ions to the system, I got this warning: