Re: [gmx-users] Topology for Sphingomyelin

On 1/22/16 7:43 PM, Ganesh Shahane wrote: Hi Justin, I have stumbled upon another problem. The sphingomyelin topology (PSM.itp) that Charmm-GUI provides has an atomtype called NHL that is not defined by the Charmm36 ff. I am using the latest charmm36-jun2015.ff. Could you please look in to thi

Re: [gmx-users] Topology for Sphingomyelin

Hi Justin, I have stumbled upon another problem. The sphingomyelin topology (PSM.itp) that Charmm-GUI provides has an atomtype called NHL that is not defined by the Charmm36 ff. I am using the latest charmm36-jun2015.ff. Could you please look in to this? On Fri, Jan 22, 2016 at 4:29 PM, Ganesh Sh

[gmx-users] gmx chi: chi.log output all rotamers always 0

hi list, using gmx chi -s file.tpr -f file.xtc -maxchi 1 -all -g -o i try to get the different rotamers and transition between them per ns. however, the chi.log output file has for every residue only this: Residue LYS12 Angle [ AI, AJ, AK, AL] rotamers 0 g(-) t g(+) ---

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93

Dear A.S. Lacey,   Along the lines of Justin's answere, you need to perform more complicated simulations.  I would suggest the 54a7 (partial atom) or CHARM36 (all atom) force fields, and add solvent and ions in a simulation box.  Once in equilibration, your structure should mimic something like

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93

On 1/22/16 3:08 PM, lloyd riggs wrote: Dear Ganesh, You can also use the ATB site, and convert the all atom .itp to CHARM36 format, or build it (charge, bond, angles, etc...) from the already present CHARMM36 atom parameters. Check your charges if you get them from the ATB. Any parameters fr

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93

Dear Ganesh,   You can also use the ATB site, and convert the all atom .itp to CHARM36 format, or build it (charge, bond, angles, etc...) from the already present CHARMM36 atom parameters.  Check your charges if you get them from the ATB.   Stephan Watkins   On 1/22/16 8:51 AM, Ganesh Shahan

Re: [gmx-users] Topology for Sphingomyelin

Thank you for your reply Justin!. It was helpful. On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul wrote: > > > On 1/22/16 8:51 AM, Ganesh Shahane wrote: > >> Dear Gromacs users, >> >> I wish to simulate a mixed lipid bilayer of which one of the lipids is >> sphingomyelin (PSM, 18:1-sphingosine an

Re: [gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations

On 1/22/16 10:04 AM, anu chandra wrote: Dear Gromcas users, I have been following the Gromcas tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/08_MD.html ) for setting up and running MD simulations of membrane proteins. I am aiming for a micros

[gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations

Dear Gromcas users, I have been following the Gromcas tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/08_MD.html ) for setting up and running MD simulations of membrane proteins. I am aiming for a microsecond long simulation. In this regard, I hav

Re: [gmx-users] Topology for Sphingomyelin

On 1/22/16 8:51 AM, Ganesh Shahane wrote: Dear Gromacs users, I wish to simulate a mixed lipid bilayer of which one of the lipids is sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using Charmm36 ff. Towards this, I constructed the bilayer using Charmm-GUI but then was surprised t

Re: [gmx-users] does gromac "mdrun" produce predicted 3d structure?

On 1/22/16 9:35 AM, Arron Lacey wrote: Thanks Justin - you mention "You need actual (extensive) MD simulations to determine that" I suppose what I am after is - what software is capable of providing such MD simulations? You've already come to the right place... -Justin Thanks! On 22/

Re: [gmx-users] does gromac "mdrun" produce predicted 3d structure?

Thanks Justin - you mention "You need actual (extensive) MD simulations to determine that" I suppose what I am after is - what software is capable of providing such MD simulations? Thanks! On 22/01/16 13:13, Justin Lemkul wrote: On 1/22/16 8:05 AM, Arron Lacey wrote: Hi everyone - I hav

[gmx-users] Topology for Sphingomyelin

Dear Gromacs users, I wish to simulate a mixed lipid bilayer of which one of the lipids is sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using Charmm36 ff. Towards this, I constructed the bilayer using Charmm-GUI but then was surprised to find that its topology is not present in res

Re: [gmx-users] does gromac "mdrun" produce predicted 3d structure?

On 1/22/16 8:05 AM, Arron Lacey wrote: Hi everyone - I have used I-TASSER to generate pdb files for missense SNPs. I understand there are some reservations about the accuracy of SNP structural changes by using homology based methods alone. Can GROMACS off anything better? I have used gmx mdrun

[gmx-users] does gromac "mdrun" produce predicted 3d structure?

Hi everyone - I have used I-TASSER to generate pdb files for missense SNPs. I understand there are some reservations about the accuracy of SNP structural changes by using homology based methods alone. Can GROMACS off anything better? I have used gmx mdrun to calculate the energy minimization

Re: [gmx-users] trivial question about water molecules

Please keep the discussion on the gmx-users mailing list. On 1/22/16 3:42 AM, Marta Wisniewska wrote: Hello Justin, thank you for your response. I know about that way. I'd like to calculate it on piece of paper. I'va already tried do this. But I have small problem and the solutions is not in a