[gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

Dear all, I was running my gromacs simulations on Gromacs 4.5.5 version but my system got updated and it changed to Gromacs 5.1.2. No when I run the same energy minimization file as earlier but just adding cutoff-scheme = Verlet, my energy minimization is not running. Following is the message

Re: [gmx-users] CG Lincs errors

As a note to Alex (and the rest of the list), the coarse-grained Martini forcefield is usually run with timesteps between 20-40 fs. 15fs is already rather low. I do agree that longer equilibration at low timestep (5 or 10) might help. Alternatively, Do you think a semiisotropic pressure coupling

[gmx-users] Manual refinement of ATB topologies ?

Hi all, I would like to know what you consider to be the ideal refinement for a topology created by ATB ? How far should we go in the manual refinement ? For instance, ATB gave me a topology for a molecule with an unsaturated acyl chain. Here are some potential issues with this topology: 1)

Re: [gmx-users] CG Lincs errors

Hi Peter, Thanks for the reply, I know we spoke in length on this mater only just recently. Many thanks for that. I’ve taken the time step of collagen in vacu down to 0.0001 and I’ve dropped the temp down to 280. I hope, running over 16 cores for two days that this should relieve any tension in

Re: [gmx-users] How to solve OXT atom (termial oxygen atom) issue?

On 12/16/16 12:33 AM, Seera Suryanarayana wrote: First of all I am extremely sorry for my mistake. I haven't sent you the modified coordinate file. I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41

Re: [gmx-users] Desolvation or hydration free energy of an ION

On 12/15/16 10:15 AM, Alex wrote: Thanks Justin for your response. Surly PMF is better, but the point is that via FEP I have already calculate the binding free energy of a charged amino acid to a solid surface while Na+ used as counter-ion where both "amino acid and Na+" considered as a

Re: [gmx-users] trajectory analysis

On 12/15/16 11:05 AM, maria khan wrote: Dear gromacs users.. I have the following questions. 1) ::how i analyse trajectory using VMD? Consult the VMD documentation, tutorials, and mailing list. 2)::Trajectory analysis for overall protein structure stability?? Define "overall protein

Re: [gmx-users] Manual refinement of ATB topologies ?

On 12/16/16 7:46 AM, Sim gmx wrote: Hi all, I would like to know what you consider to be the ideal refinement for a topology created by ATB ? How far should we go in the manual refinement ? For instance, ATB gave me a topology for a molecule with an unsaturated acyl chain. Here are some

[gmx-users] normalized

I have asked this question a few days back; I try one more time: When I am trying calculate the degrees of overlap of subsets of a simulation to the whole trajectory by following the explanation in the manual gmx anaeig: "When -v, -eig, -v2 and -eig2 are given, a single number for the overlap

Re: [gmx-users] Charge Correction using HF method

On 12/16/16 2:54 AM, tasneem kausar wrote: Dear Justin Sir I am doing protein and drug MD simulation. I have generated the itp file of drug from PRODRG. I have calculated the charge on the atom using HF/6- 31G* basis set from orca3.0. Is this a right protocol to use it in GROMACS for the

[gmx-users] How to resolve OXT atom issue?

Dear Justin, I apologize you as I am wasting your valuable time. I have peptide with 69 residues and some of the SER and THR residues are phosphorylated and also some of the missing residues(1 to 6; 36 to 41 and 69) have been modeled by modeller . I have chosen charmm36 force field.

Re: [gmx-users] How to resolve OXT atom issue?

I think you can go for Swissviewer rather going for modeller On Sat, 17 Dec 2016 at 12:04 PM, Seera Suryanarayana wrote: > Dear Justin, > > > > I apologize you as I am wasting your valuable time. > > > > I have peptide with 69 residues and some of the SER and THR residues