[gmx-users] lipid / -OH oscillation period

Hi, I have a protein/lipid system. Using charmm36 ff and gromacs5.1.4. I set constraints = h-bonds because of charmm. 1. After that grompp complains about the oscillation between an O and H in the lipid. Why? It should not. Possible explanations I can imagine: - does gromacs constrain only pro

[gmx-users] regarding posting queries in gromacs mailing list

Dear Gromacs developers, Following is my email address for posting queries to GROMACS srivastav...@iitj.ac.in Best regards, *Abhinav Srivastava* *Research Scholar* Indian Institute of Technology, Jodhpur Rajasthan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs

Re: [gmx-users] regarding posting queries in gromacs mailing list

Hi, You have already subscribed, nothing else is needed. Mark On Mon, 8 May 2017 13:44 Abhinav Srivastava (P14CHM002) < srivastav...@iitj.ac.in> wrote: > Dear Gromacs developers, > > Following is my email address for posting queries to GROMACS > srivastav...@iitj.ac.in > > Best regards, > > *Ab

Re: [gmx-users] lipid / -OH oscillation period

On 5/8/17 4:32 AM, Tamas Hegedus wrote: Hi, I have a protein/lipid system. Using charmm36 ff and gromacs5.1.4. I set constraints = h-bonds because of charmm. 1. After that grompp complains about the oscillation between an O and H in the lipid. Why? It should not. Possible explanations I can i

Re: [gmx-users] question about applying surface tension

On 5/7/17 2:56 PM, Ali Shomali wrote: Thanks so much Justin for your answer. actually I performed different simulations and compared the area per lipid with existing studies . for example I used gromacs charmm 22 for DPPC simulation and compared the results with Dr.Feller's paper. also I conduc

Re: [gmx-users] ligand moving out during umbrella sampling

On 5/7/17 2:22 PM, abhisek Mondal wrote: Hello Justin, Thank you for the explanation. I'm really new to the field so choosing factors in a bit confusion. You said in this set up the ligand can still move around X and Y direction. My question is what if I set pull_k1=0? The ligand also won't mo

[gmx-users] Ligand Boron parameters

Good afternoon, I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a boron atom. Can anyone help me or give me some information how can I do the parameterization of the ligand. Best Regards, Pedro Fernandes -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] ligand moving out during umbrella sampling

On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote: > > > On 5/7/17 1:57 AM, abhisek Mondal wrote: > >> Hi, >> >> For your ease of understanding regarding what is happening during this >> above said umbrella-mdrun, I have shared the trajectory video file the >> following link. >> https://drive.

Re: [gmx-users] Error In Umbrella sampling.

Every time I ran through this step I needed to use -maxwarn. It raises no issues later on. On Fri, Apr 14, 2017 at 11:42 PM, Thomas Piggot wrote: > I too also fairly frequently use the -maxwarn option for this message. > Perhaps it would be better off as a grompp note rather than a warning, or >

Re: [gmx-users] Ligand Boron parameters

On 5/8/17 9:04 AM, Pedro Fernandes wrote: Good afternoon, I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a boron atom. Can anyone help me or give me some information how can I do the parameterization of the ligand. The details will depend on the force field yo

Re: [gmx-users] ligand moving out during umbrella sampling

On 5/8/17 10:00 AM, abhisek Mondal wrote: On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul wrote: On 5/7/17 1:57 AM, abhisek Mondal wrote: Hi, For your ease of understanding regarding what is happening during this above said umbrella-mdrun, I have shared the trajectory video file the foll

[gmx-users] Internal energy

Hi gromacs user, A peptide(p), a solid surface(s) in water(w) solution are the three ingredients of my system. The total internal energy (Utot) of the system in NVT ensemble, can be defined as Utot = Upp + Uww + Upw + Usw + Ups , where the Uxy is the internal energy of interaction between x and y.

[gmx-users] gmx cluster -binary flag to get the "centroid" as the member that has max neighbours < cutoff ?

Dear users: I have a bunch of trajectories of the same system. I want to cluster them together (using gmx cluster gromos algorithm), identify the centroids, and then use gmx rms to evaluate the RMSD to the centroid of the top N clusters in each trajectory. The reason I want to do this is to be