[gmx-users] Topology generation of molecules

If PRODRG is not giving suitable results . Can I use Antechamber output in GROMACS for the topology generation of molecules ?  . Regards,  ___                     ABID  ALI Junior Research Fellow, Lab No.  P-133, Computational Chemistry Unit, Dr

Re: [gmx-users] Regarding Creating a molecule and fitting it to CHARMM forcefield

Hi, See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation Mark On Tue, 20 Jun 2017 06:49 Dilip H N wrote: > Hello all, > I want to create a molecule (methylamine) and want to run the simulation > in CHARMM forcefield.. > 1] How can i create

[gmx-users] Regarding Creating a molecule and fitting it to CHARMM forcefield

Hello all, I want to create a molecule (methylamine) and want to run the simulation in CHARMM forcefield.. 1] How can i create the molecule methylamine such tht its residues fit into CHARMM forcefield..?? 2] How do i get its topology/itp for running the simulation..??? 3] If the required molecule

[gmx-users] RMSD output from gmx confrms differs from gmx rms?

Hello: I would like to measure the C RMSDs between structures from a trajectory and a PDB structure. With gmx rms, I get warning messages about different number of atoms in the input files. So I create pdb files from the trajectory, with solvent excluded. But when I run gmx confrms with these

Re: [gmx-users] Unable to generate umbrella histogram and PMF curve

On 6/19/17 8:52 PM, Norfarisha Mohd Fadil wrote: Dear users, I ran a WHAM analysis after umbrella sampling simulation, and this error occurred: Reading pull force file with pull geometry distance and 1 pull dimensions Expecting these columns in pull file: 0 reference columns for each

Re: [gmx-users] 5' phosphate of RNA

On 6/19/17 8:55 AM, Mohammad fat habadi wrote: DEAR Users I have a RNA that has phosphate(P,OP,OP2,OP3) on 5’. IN RNA and DNA, 3’ has phosphate and 5‘ doesn’t it and for this all Force fields don’t know phosphate atoms on 5’ of RNA. pdb2gmx make an error. IF I delete 5’ phosphate atoms, I

[gmx-users] Unable to generate umbrella histogram and PMF curve

Dear users, I ran a WHAM analysis after umbrella sampling simulation, and this error occurred: Reading pull force file with pull geometry distance and 1 pull dimensions Expecting these columns in pull file: 0 reference columns for each individual pull coordinate 1 data columns for

Re: [gmx-users] distance restraint in gromacs md run

Hi, On Mon, 19 Jun 2017 15:54 Simon Kit Sang Chu wrote: > Hi Mark, > > I thought including distance restraint file here would still be valid? > It is valid. I think Justin overlooked how you separated the different content from different files. Although this is called

Re: [gmx-users] error in phosphoserine simulation during MD

Hi, You need to use a tool capable of doing the job. But it is unclear to anyone reading this how phosphoserine relates to the problem, or what loop needs to be built. Mark On Sun, 18 Jun 2017 22:07 marzieh dehghan wrote: > thank you very much > > I tried to complete

Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

Hi, We can't support third party build guides, but please follow ours and ask questions about it here. Provide full details. Mark On Mon, 19 Jun 2017 23:39 Guyen Gn wrote: > I have used the Nvidia's gromacs page to buid and run the gromacs. > Few months back, I have used

[gmx-users] AVX related compiler error during build with P100 RHEL7

I have used the Nvidia's gromacs page to buid and run the gromacs. Few months back, I have used the Xeon CPU to build and run successfully on RHEL7.2. This also used the M6 GPU card. Now the same build is failing with AVX related compiler error if I use latest Skylake processor and P100 GPU. I

[gmx-users] a problem about ewald geometry=3dc

Hello to all Dear Gromacs Users I'm modeling a lipid monolayer with vacuum space on top of it and with periodic boundary conditions in xyz directions. the vacuum space is about 10nm to minimize any possible effect of periodicity. for using ewald summation as manual mentions : *"The geometry to

[gmx-users] a problem about ewald geometry=3dc

Hello to all Dear Gromacs Users I'm modeling a lipid monolayer with vacuum space on top of it and with periodic boundary conditions in xyz directions. the vacuum space is about 10nm to minimize any possible effect of periodicity. for using ewald summation as manual mentions : *"The geometry to

[gmx-users] a problem about ewald geometry=3dc

Hello to all Dear Gromacs Users I'm modeling a lipid monolayer with vacuum space on top of it and with periodic boundary conditions in xyz directions. the vacuum space is about 10nm to minimize any possible effect of periodicity. for using ewald summation as manual mentions : *"The geometry to

Re: [gmx-users] MD run error

Hi, What are you simulating, with what model physics? Mark On Mon, 19 Jun 2017 21:13 Mishelle Oña wrote: > Hi, > > I got this error. Can anyone explain me what it means. > > WARNING: This run will generate roughly 10571 Mb of data > > starting mdrun 'UNITED ATOM

[gmx-users] MD run error

Hi, I got this error. Can anyone explain me what it means. WARNING: This run will generate roughly 10571 Mb of data starting mdrun 'UNITED ATOM STRUCTURE FOR MOLECULE LIG in water' 1000 steps, 2.0 ps. NOTE: Turning on dynamic load balancing DD cell 3 0 0: Neighboring cells do not

[gmx-users] Computing work from pulling simulations

I am using “umbrella pulling” to simulate the dissociation of two molecules. I would like to calculate the work W(t) that the harmonic trap has performed on my system up to timestep t, which can be calculated as W(t) = sum_{i=0}^t F_i * v * dt where F_i is the biasing force at timestep i, v is

Re: [gmx-users] Temperature control in fix gcmc with fix rigid/nvt/small

Sincere apologies to this unrelated post to the mailing system. Please just ignore it! In fact, when I decided to post a problem that troubles me recently, I opened then mail client and by coincidence I was just clicking on the gromacs mailing list which do me a regular push service and thus

[gmx-users] phosphate atoms on 5' Of RNA

Dear Users I has a RNA that has phosphate atoms (P,OP1,OP2,OP3) on 5'.Most RNA and DNA have phosphate atoms on 3'  not on 5' and for this all force fields don't know phosphate atoms on 5' of RNA. pdb2gmx make  errors like: OP3 atom isn't  on rtp file .If I delete phosphate atoms from 5' of RNA

[gmx-users] xx inconsistent shift check your topology

Dear Gromacs users, I am simulating a silica slab and get a warning stating there are “xx inconsistent shifts, check topology”. In my .mdp file I already have periodic-molecules=yes. Is this a common error? Do you recommend any approach to finding what causes it? Thank you, Amanda -- Gromacs

[gmx-users] 5' phosphate of RNA

DEAR Users I have a RNA that has phosphate(P,OP,OP2,OP3) on 5’. IN RNA and DNA, 3’ has phosphate and 5‘ doesn’t it and for this all Force fields don’t know phosphate atoms on 5’ of RNA. pdb2gmx make an error. IF I delete 5’ phosphate atoms, I don’t have any problems. How can I solve this

Re: [gmx-users] Coulomb values

On 6/19/17 5:43 AM, Merril Mathew wrote: Dear Gromacs users, I was trying to extract electrostatics and van der Waals interactions for specific lipid molecules in the system I simulated. I assume you can get the coulomb and LJ values from energy. But why is there more than one options to

Re: [gmx-users] distance restraint in gromacs md run

On 6/19/17 1:51 AM, Simon Kit Sang Chu wrote: Hi, I have a protein of interest which requires distance restraint for C alpha atoms. However, the simulation does not seem to include the restraint at all. *prod.mdp* define = -DPOSRES constraints = none integrator

Re: [gmx-users] hydrogen bond analysis

On 6/19/17 3:49 AM, João Henriques wrote: Dear Imrul, I believe the information you seek is right there in your xvg file header: @xaxis label "Time (ns)" @yaxis label "Number" ... @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" First column is always time

[gmx-users] Pull in a channel

Hi All, I would like to pull a ligand in a channel from my protein and calculate the PMF with Umbrella sampling. How to define in the md_pull.mdp configuration file all the transition points of my pathtway through which my ligand must pass ? This channel is not rectilinear and is the result

[gmx-users] Coulomb values

Dear Gromacs users, I was trying to extract electrostatics and van der Waals interactions for specific lipid molecules in the system I simulated. I assume you can get the coulomb and LJ values from energy. But why is there more than one options to select for both Coulomb and LJ from the list.?

Re: [gmx-users] hydrogen bond analysis

Dear Imrul, I believe the information you seek is right there in your xvg file header: @xaxis label "Time (ns)" @yaxis label "Number" ... @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" First column is always time (x-axis). All other columns are y-axes for different

Re: [gmx-users] Temperature control in fix gcmc with fix rigid/nvt/small

It may come as a huge surprise, but this is a mailing list for a different software package. ;) On 6/19/2017 12:49 AM, Youzhi Hao wrote: hi, I'm trying to do gcmc simulation of rigid CH4 molecules adsorption isotherms in clay minerals by using fix gcmc with fix rigid/nvt/small. The coulomb

[gmx-users] Temperature control in fix gcmc with fix rigid/nvt/small

hi, I'm trying to do gcmc simulation of rigid CH4 molecules adsorption isotherms in clay minerals by using fix gcmc with fix rigid/nvt/small. The coulomb potential was calculated by PPPM. The fix rigid/nvt/small was combined with fix_modify dynamic/dof yes and fix_modify temp as the LAMMPS