[gmx-users] Suggestion required for calculation of membrane contact sites and Lipid binding strength

Dear Gromacs users, Can anyone suggest me a way to find the membrane contact sites i.e. the lipids that are making contact with protein residues with respect to time from a membrane protein simulation? I have calculated the distance and contact of protein residues from upper leaflet atoms of

[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

Dear Mark, Thanks for the suggestion. I will tell them that. Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- Gromacs Users mailing list * Please search the

[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

Dear Mark, I will ask our HPC support team to check the MPI enabled version of gromacs then. Thank you for your suggestion. Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M :

[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

Dear Users, I was trying to do equilibration of a mixed lipid vesicle using gromacs 5.1 in parallel using the below pasted pbs script : #!/bin/tcsh #PBS -l walltime=48:00:00 #PBS -N VES_new_16 #PBS -q workq #PBS -l select=1:ncpus=16:mpiprocs=16 #PBS -V # Go to the directory from which you

[gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel

Dear Gromacs users, I was trying to do equilibration of a mixed lipid vesicle using gromacs 5.1 in parallel. My pbs script file details for this is the following : /home/lipi/openmpi164/bin/mpirun -np 48 /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm step6.2_equilibration -rdd 1.8

[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system

Dear gromacs users, I am trying to calculate domain decomposition of a mixed lipid vesicle system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to run in parallel. I want to calculate the number of PME nodes per total number of nodes. However, i am not clear on how to

[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

Dear Mark, I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom system. What further could be done? Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M :

[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

Dear Sir, The MD.trr i expect to be having 382ns of data as is mentioned in the log file and MD.xtc that was generated alongwith MD.trr when the simulation ran has 382ns. However, MD.trr has problems in giving output beyond 25ns. Could it be corruption of frames or something? Kind Regards,

[gmx-users] help required in plotting percentage of protein in contact with membrane vs time

Dear Gromacs users, I have a membrane protein simulation performed with gromacs 4.6. I have calculated the minimum distance of protein residues from upper leaflet of the lipid bilayer. I also have the time wise atom pair contacts as an output. The following command i used : g_mindist -f

[gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

Dear gromacs users, I was trying to dump structures from MD.trr using trjconv. The MD.trr has 0ns to 382ns of data. (i checked the MD.log file also). However, when i try to dump structures beyond 25ns, with the following command : *gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr

[gmx-users] help required in calculating npme value for domain decomposition

Dear gromacs users, I need help in calculating the value of npme for the purpose of domain decomposition for my system of mixed lipid vesicles. Thanks!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- On Thu, May 19, 2016 at 6:35 PM, Antara mazumdar <antara.mazum...@igib.in> wrote: > Dear gromacs users, > > I have a peripheral membrane protein which I have simulated using Charmm > 36 in

[gmx-users] Help required for calculation of protein coverage % wrt time

to go about it after this? Antara Mazumdar ISCB SC RSG-India Core Committee Member -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 55

> > need to look at observables to judge that it's equilibrated. Their > builder > > should provide reasonable defaults, but you can't assume they're perfect, > > either. In particular, if the last equilibration ensemble doesn't match > the > > production ensem

[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

Dear users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model 2.2. I have already performed all the equilibration steps successfully on my desktop with GROMACS 5.1.0. However, when i try to execute its production run in

Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar <antara.mazum...@igib.in> wrote: > Dear gromacs users, > > I am trying to r

[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

Dear gromacs users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model. I have already performed all the equilibration steps successfully on my desktop. However, when i try to execute its production run in parallel it complains of

[gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations

i want to simulate a system having membrane and proteins with pbc=no to allow surface effects. I use the following settings in my production mdp file : Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 ms dt =

[gmx-users] error in grompp : Something is wrong in the coordinate formatting of file system.gro

Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting *Something is wrong in the

[gmx-users] error in grompp : No such molecule type Protein

Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting No such molecule type

[gmx-users] query regarding coarse grained simulation of a peripheral membrane protein

​Hi, How do i generate a topology file of a peripherally attached dimeric protein with a homogenous lipid bilayer using coarse grained approach? ​i have concatenated the coarse grained structure of lipids and protein prior to this. -- *Best,* *Antara* -- J.R.F.(Project) Systems Biology Group

[gmx-users] Need of mdp files

Hi, I am trying to simulate a peripheral membrane protein in a heterogenous lipid bilayer of DOPC and DOPG using charmm 36 force field in GROMACS. i need mdp files for NPT, NVT, steep and MD to check whether the conditions i am using to simulate my system are appropriate or not. -- Regards,

[gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints

Hi, I minimised a heterogenous lipid system of 1464 DOPC and DOPG and applied position restraints as well as had vdwradii.dat file for genbox step. Yet after minimisation, there are gaps between the lipid molecules. Pls suggest a remedy. -- Regards, Antara -- J.R.F.(Project) Systems Biology

[gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS

​eRROR OBTAINED DURING NVT: ​ Water molecule starting at atom 673675 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. ​NVT CONDITIONS WERE : ​ n for B2AR-POPC system define = -DPOSRES ; Protein is position restrained (uses the posres.itp file

[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg

i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with