Re: [gmx-users] CHARMM36 parameter for polysaccharide branching

Thanks Justin :) It worked. Small numbers!!! Best, MH > On May 25, 2017, at 3:29 PM, Justin Lemkul wrote: > > > > On 5/25/17 3:00 PM, Mohammad Hassan Khatami wrote: >> Hello! >> I am trying to simulate a simple branching polysaccharide molecule. Thanks >> to you, I found and

Re: [gmx-users] RMSF per residue

Thanks Justin! On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul wrote: > > > On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> I have a question on RMSF calculation: >> >> I am not sure how -res works in RMSF and I could not find any useful >>

Re: [gmx-users] simulating AMP covalently linked to a protein

On 5/25/17 3:12 PM, Gilberto Valdes wrote: Thanks for your answer, I would like to use charmm27 force field, it covers the hole AMP molecule if I use the ADE residue with the 5PHO and 3TER patches implemented in charmm software. The problem is how to patch the ADE equivalent residue (named RA)

Re: [gmx-users] CHARMM36 parameter for polysaccharide branching

On 5/25/17 3:00 PM, Mohammad Hassan Khatami wrote: Hello! I am trying to simulate a simple branching polysaccharide molecule. Thanks to you, I found and implemented the CHARMM36 parameters for the 1->4 and 1->6 links, however, I was not able to find the exact partial charge parameters for

Re: [gmx-users] simulating AMP covalently linked to a protein

Thanks for your answer, I would like to use charmm27 force field, it covers the hole AMP molecule if I use the ADE residue with the 5PHO and 3TER patches implemented in charmm software. The problem is how to patch the ADE equivalent residue (named RA) in gromacs, and then how to linked to the

[gmx-users] CHARMM36 parameter for polysaccharide branching

Hello! I am trying to simulate a simple branching polysaccharide molecule. Thanks to you, I found and implemented the CHARMM36 parameters for the 1->4 and 1->6 links, however, I was not able to find the exact partial charge parameters for the monomer in the branching point of the polymer. In

Re: [gmx-users] DSSP

On 5/25/17 12:08 PM, Mariusz Wierzbowski wrote: Hi, I would like to analyze secondary structure elements for my protein. I want to do it with do_dssp command in gromacs. I am using gromacs on a plgrid platform. The problem is that an error occurs: Fatal error: DSSP executable

Re: [gmx-users] em and nvt problem

On 5/25/17 7:12 AM, Kashif wrote: Hi Whenever I tried to simulate one of my docked complex, the energy minimization step converged very fast and complete at 112 steps. And when I proceed with NVT equilibration I got split structures like step4b_n6.pdb step4c_n6.pdb step5b_n6.pdb

Re: [gmx-users] Check stability of complex

On 5/25/17 5:19 AM, Kashif wrote: Hi I have simulated my protein drug complex for 20 ns. My protein size was actually 600 amino acid residues but I have simulated only docked portion of my protein which was only about 300 aa residues. Now I want to see the effect of rest of my protein

Re: [gmx-users] gromacs bond energy calculate

On 5/25/17 3:57 AM, 王珍 wrote: Hi all, Recently i want to cauculate the bond energy and angle energy for my RNA system, and the RNA was simulated by gromacs about 100 ns, could I use the command of gromacs to calculate the bond energy and angle energy for the RNA residues in my all-atom

Re: [gmx-users] simulating AMP covalently linked to a protein

On 5/24/17 7:08 PM, Gilberto Valdes wrote: Hi, I'm interested in simulating a DNA ligase with an AMP bound covalently via its P atom to the side chain of a Lysine residue. I can not find any parameters for that. I really appreciate any help in how to achieve this.

Re: [gmx-users] RMSF per residue

On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote: Dear Gromacs users, I have a question on RMSF calculation: I am not sure how -res works in RMSF and I could not find any useful explanation for it. It will give the average fluctuations per residue, fine. but how exactly? 1) it calculates the

[gmx-users] Nose-Hoover + acc-grps

Hello, I'm trying to run non-equilibrium simulations in the NVT ensemble with the "acc-grps" command and the Nose-Hoover thermostat, but I know that there are ways in which an external acceleration can be incompatible with Nose-Hoover. Are these two compatible in the Gromacs code? Thank you,

[gmx-users] DSSP

Hi, I would like to analyze secondary structure elements for my protein. I want to do it with do_dssp command in gromacs. I am using gromacs on a plgrid platform. The problem is that an error occurs: Fatal error: DSSP executable (/opt/dssp/bin/dssp) does not exist (use setenv DSSP). On

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

On Thu, May 25, 2017 at 2:09 PM, Marcelo Depólo wrote: > Hi, > > > I had the same struggle benchmarking a similar system last week. Just for > curiosity, could you tell us the performance you get when sharing your GPU > with multiple jobs? BTW, interpreting some

Re: [gmx-users] em and nvt problem

You can try to reduce emtol in your minimization parameters or start your nvt at a different, lower, temperature. Best, Marlon Sidore PhD Student Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2017-05-25

Re: [gmx-users] em and nvt problem

It would be helpful if you include the output of the em run and the log file for the nvt run. Best, Dan On Thu, May 25, 2017 at 7:12 AM, Kashif wrote: > Hi > Whenever I tried to simulate one of my docked complex, the energy > minimization step converged very fast

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

On Thu, May 25, 2017 at 2:09 PM, Marcelo Depólo wrote: > Hi, > > > I had the same struggle benchmarking a similar system last week. Just for > curiosity, could you tell us the performance you get when sharing your GPU > with multiple jobs? > > In my case (6k atoms +

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

Hi Marcelo, That sounds reasonable depending on your time-step and other factors, but I have not attempted to run with more than one job for GPU. Maybe Mark can comment more. Best, Dan On Thu, May 25, 2017 at 8:09 AM, Marcelo Depólo wrote: > Hi, > > > I had the same

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

Hi, I had the same struggle benchmarking a similar system last week. Just for curiosity, could you tell us the performance you get when sharing your GPU with multiple jobs? In my case (6k atoms + Reaction field + 8 cores 2.2Ghz + TitanX Pascal), I've got ~440 ns/day. However, I get ~280 ns/day

[gmx-users] em and nvt problem

Hi Whenever I tried to simulate one of my docked complex, the energy minimization step converged very fast and complete at 112 steps. And when I proceed with NVT equilibration I got split structures like step4b_n6.pdb step4c_n6.pdb step5b_n6.pdb step5c_n6.pdb I have already docked the

[gmx-users] Check stability of complex

Hi I have simulated my protein drug complex for 20 ns. My protein size was actually 600 amino acid residues but I have simulated only docked portion of my protein which was only about 300 aa residues. Now I want to see the effect of rest of my protein sequences on the stability of this 300 aa+drug

Re: [gmx-users] gromacs bond energy calculate

Hi Jane, I don't know if you can do that with one of Gromacs tools, but you can easily extract your bond length/angle values as a function of time with gmx distance and gmx angle, respectively. Then, knowing the formula for bond and angle energies as well as parameters (force constants and

[gmx-users] gromacs bond energy calculate

Hi all, Recently i want to cauculate the bond energy and angle energy for my RNA system, and the RNA was simulated by gromacs about 100 ns, could I use the command of gromacs to calculate the bond energy and angle energy for the RNA residues in my all-atom molecular dynamics simulation?

Re: [gmx-users] gromacs-5.1.4 installation issue

Hi, Yes, those are from the standard system compiler, which obviously doesn't work. You're not using that compiler, so you need to know how the one you are using should be used and where its standard library is and why the clusters are not actually identical because one compiler works and one

Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

Hi, Good. Remember that the job scheduler is a degree of freedom that matters, so how you used it and why would have been good to mention the first time ;-) And don't just set your time step to arbitrary numbers unless you know why it is a stable integration scheme. Mark On Thu, May 25, 2017 at

Re: [gmx-users] gromacs-5.1.4 installation issue

On Wed, May 24, 2017 at 6:08 PM, Mark Abraham wrote: > Hi, > > You should ask the cluster maintainers how they intend the compiler to be > used. You need to find the same infrastructure at run time as you used at > compile time, e.g. by loading the same modules. > > Yes

[gmx-users] grompp error

Hi GROMACS users,   I want to simulate a graphene sheet, and I want to use OPLS-AA force field. So, I copied the forcefield in my directory and changed some the files in it (ffbonded.itp, ffnonbonded.itp, atomtype.atp, aminoacids.rtp, and atomname2type.n2t). I used the pdb2gmx command to