Re: [gmx-users] Modifying force field for graphene

Thank you very much Alex. Mohammad From: Alex To: gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪ Sent: Tuesday, 11 July 2017, 22:54:56 Subject: Re: [gmx-users] Modifying force field for graphene The answer is yes, OPLSAA does need to be

[gmx-users] RDF

Hi, I want to calculate RDF of my organic molecule with a solvent. What should be the duration of my simulation? Is 100 ps enough? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Accessible Surface Area (ASA) for each residue per frame

Hi there, Is there a way using gmx sasa or gmx do_dssp to get the ASA per residue per frame? I only find option to extract the average over all frames per residue. Thanks, Max -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

hBN is hardly a common subject of simulation for Gromacs folks, but let's see... 1. When you run the simulation in vacuum, do you get the same error? Does a 300K vacuum simulation result in reasonable sheet behavior? What about NVT? 2. What GROMACS forcefield are you using and what are the

[gmx-users] Periodic Molecule's Free Energy Calculation Error

Hello Gromacs Community, I am trying to calculate the solvation free energy of a hBN sheet following Justin Lemkul and Alchemistry's tutorials. Since the hBN sheet is infinitely large, I turned the periodic molecules flag on. This runs all fine on one core, but when I try to run NVT in parallel

Re: [gmx-users] Concrete pull code explanation needed

> On 7/10/17 11:19 PM, Du, Yu wrote: > > Dear Justin and gmx users, > > > > > > I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial > > serveral times. > > > > > > The following is Justin's pull code. > > > > > > ; Pull code > > pull= yes > >

Re: [gmx-users] output pdb reformatted

You are absolutely right once again. I've been glancing over that topology, looking right at what the problem was, and not seeing it. The residue name column was empty, all atom types went to crap, but because I always grompp with -maxwarn 10 (for completely unrelated warnings in completely

Re: [gmx-users] output pdb reformatted

On 7/11/17 4:01 PM, Alex wrote: Hi all, I have a tiny acetonitrile molecule here. The input pdb prior to EM is this: TITLE Gromacs Runs On Most of All Computer Systems REMARKTHIS IS A SIMULATION BOX CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 MODEL1 ATOM 1

Re: [gmx-users] DNA topology error

On 7/11/17 3:40 PM, maria khan wrote: dear Mark Abraham According to my error like """Residue 9 named DG of a molecule in the input file was mapped to an entry in the topology database, but the atom O5' used in that entry is not found in the input file. Perhaps your atom and/or residue

Re: [gmx-users] RDF

On 7/11/17 1:38 PM, Pandya, Akash wrote: When I try to make an index group for the protein residue and the ligand molecule, the whole system is included in the index file. I use these options: r 166 (protein residue) r 901 (ligand molecule) then press q All the default groups will

Re: [gmx-users] umbrella sampling

On 7/11/17 1:38 PM, Ben Tam wrote: Hi Justin, I am trying to get an energy profile when water molecules go through the porous cage. I am restraint it to z direction because I would like to see the energy that require to jump from one cage to another. I set up the simulation so that the

[gmx-users] Gmx 2016.3 compilation error on PHI

Hi all. I'm having some issues while trying to compile the Gromacs 2016.3 version for a Xeon Phi Knights *Corner* (not Landing). I'm running the latest version of cmake (own compilation, worked on other compilations done previously: 5.1.2 on gcc and 2016.3 on gcc and icc) with the following line

[gmx-users] output pdb reformatted

Hi all, I have a tiny acetonitrile molecule here. The input pdb prior to EM is this: TITLE Gromacs Runs On Most of All Computer Systems REMARKTHIS IS A SIMULATION BOX CRYST1 30.000 30.000 30.000 90.00 90.00 90.00 P 1 MODEL1 ATOM 1 CT ACT 1 14.870 14.744

[gmx-users] DNA topology error

dear Mark Abraham According to my error like """Residue 9 named DG of a molecule in the input file was mapped to an entry in the topology database, but the atom O5' used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.""" if O5' can be set

Re: [gmx-users] Modifying force field for graphene

The answer is yes, OPLSAA does need to be slightly edited for graphene and nanotubes to work, assuming you find good parameters for graphene. Google is strong with you, use it. Alex On 7/11/2017 8:34 AM, ‪Mohammad Roostaie‬ ‪ wrote: Hi All, I want to simulate graphene by using OPLS_AA force

Re: [gmx-users] RDF

When I try to make an index group for the protein residue and the ligand molecule, the whole system is included in the index file. I use these options: r 166 (protein residue) r 901 (ligand molecule) then press q Akash -Original Message- From:

Re: [gmx-users] umbrella sampling

Hi Justin, I am trying to get an energy profile when water molecules go through the porous cage. I am restraint it to z direction because I would like to see the energy that require to jump from one cage to another. I set up the simulation so that the structure is repeated at z direction

Re: [gmx-users] umbrella sampling

On 7/11/17 12:53 PM, Ben Tam wrote: Hi Andre, Thanks for your answer. Actually I should clarify it is metal-organic-framework that I am working on which is a porous material. With the k value larger than 100, the histogram become multiple sharp single peak. Furthermore when I look at

Re: [gmx-users] RDF

On 7/11/17 11:41 AM, Pandya, Akash wrote: Hi, I want to calculate the RDF between a specific residue and a ligand molecule in my simulation box. Is this possible and do I have to make a special index group for that? If so how would I go about doing that? By using make_ndx or a suitable

Re: [gmx-users] Modifying force field for graphene

On 7/11/17 10:34 AM, ‪Mohammad Roostaie‬ ‪ wrote: Hi All, I want to simulate graphene by using OPLS_AA force field. Does this force field need any modification for graphene simulation?If yes, do you have any link tutorial for the modification? What do you find when investigating the

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

On 7/11/17 7:06 AM, mohammad fathabadi wrote: Thank you Justin I saw SOMNATH question and your answer about 5' PHO on 5 Jul. According that answer, I put PRES 5 PHO from top_all36_na.rtf file in merged.n.tdb file after [5TER] section but I receive many errors like: Atom NA not found in

Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

On 7/11/17 2:46 AM, Akash Ranjan wrote: Sir, I am facing difficulty in making topology for a simple molecule using CHARMM36 but i am facing certain difficulty in that such as (a)Warning: Long Bond (3-10 = 0.566378 nm) Warning: Long Bond (3-4 = 0.426475 nm) Warning: Long Bond (4-16 = 0.59

Re: [gmx-users] Concrete pull code explanation needed

On 7/10/17 11:19 PM, Du, Yu wrote: Dear Justin and gmx users, I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial serveral times. The following is Justin's pull code. ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1

Re: [gmx-users] ligan minimization in vacuo

On 7/10/17 5:57 PM, ‪farial tavakoli‬ ‪ wrote: Dear gmx-users I have a problem in equilibration my protein-ligand complex and encountered to this error after 2 steps of 5 steps:one or more water molecules can not be settled. check for bad contacts or reduce the time steps. so I decided

Re: [gmx-users] Acetonitrile using CHARMM ff

On 7/10/17 10:52 AM, Sonia Milena Aguilera Segura wrote: Dear Justin, Thank you for the answer. I changed the two parameters suggested in the mdp file and I ran again a minimization, 200 ps NVT, 200 ps NPT, and 1 ns MD for the two cases of the previous mail, and now I am getting densities

Re: [gmx-users] Generating GROMACS input file from the GAMESS output file

On 7/10/17 2:32 AM, 조영래 wrote: Thank you Justin Every time your comment helped me. I should compare two system that are Zn_binding protein and Fe_binding protein. So I need force field that satisfies the following conditions. First, force field contains two metal ion (Fe and Zn)information.

Re: [gmx-users] umbrella sampling

Hi Andre, Thanks for your answer. Actually I should clarify it is metal-organic-framework that I am working on which is a porous material. With the k value larger than 100, the histogram become multiple sharp single peak. Furthermore when I look at individual 0.1nm slides, it runs completely

Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there' s a lot of room inside a crystal for any molecule to diffuse there, especially when it comes to cross something like a crystallographic plane, meaning that huge energy barriers should be there, leading to NaN and other

[gmx-users] umbrella sampling

Dear All, I am doing umbrella sampling for a water molecules moving inside a crystal structure, however I am running into a problem on the output file with profile.xvg all value showing “nan”. This error has occurred when I reduce the slide width from 0.2 nm to 0.1 nm. I have used the exact

Re: [gmx-users] DNa topology error.

Hi, pdb2gmx found a residue called DG and found an rtp entry that matched it. It just didn't find an O5' atom within it. You should also be able to find that residue. Mark On Tue, Jul 11, 2017 at 5:26 PM maria khan wrote: > Thanks Mark Abraham. > > i would like to

[gmx-users] RDF

Hi, I want to calculate the RDF between a specific residue and a ligand molecule in my simulation box. Is this possible and do I have to make a special index group for that? If so how would I go about doing that? Thanks, Akash -- Gromacs Users mailing list * Please search the archive at

[gmx-users] DNa topology error.

Thanks Mark Abraham. i would like to share my pdb file as still i dont understand the error as well as your answer,kindly look at this then explain it. it cant be shared as the file is large.i checked the file in front of residue 9,there is no DG at all .All along the chains is DA. regards. --

[gmx-users] Modifying force field for graphene

Hi All, I want to simulate graphene by using OPLS_AA force field. Does this force field need any modification for graphene simulation?If yes, do you have any link tutorial for the modification? Kind regards,Mohammad -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Problem reading pdb files

Hi, I imagine that at least one of the trajectories did not have a good PCA analysis because you probably want both trajectories such that molecules are whole with respect to PBC. The frame from the second trajectory is not. There's a useful workflow at

Re: [gmx-users] problem: gromacs run on gpu

Hi, Making your run stay to the cores it is assigned is always a good idea, and using -pin on is a good way to do it. If there's more than that job on the node, then it is more complicated than that. More information here

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

Hi, I'm genuinely curious about why people set ewald_rtol smaller (which is unlikely to be useful, because the accumulation of forces in single precision will have round-off error that means the approximation to the correct sum is not reliably accurate to more than about 1 in 1e-5), and thus

Re: [gmx-users] Error of DNA topology

Hi, Like it says, you'll need to understand why pdb2gmx expects O5' but your coordinate file doesn't have one. We can't see your files or understand the context of residue 9. Mark On Tue, Jul 11, 2017 at 2:14 PM maria khan wrote: > Dear gromacs user. > > i am

Re: [gmx-users] Using an rtp file in an non standard directory

Hi, Make a copy of the whole forcefield. See http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Modifying_a_force_field Mark On Tue, Jul 11, 2017 at 2:51 PM Miguel Caro wrote: > Hello, > > I have created my own rtp file which I want to use in

[gmx-users] Using an rtp file in an non standard directory

Hello, I have created my own rtp file which I want to use in conjunction with the OPLS force field. If I understand it correctly, the easiest way to get pdb2gmx to build my topology would be to copy my rtp file into the oplsaa.ff/ directory, and Gromacs looks for my molecule name inside anything

[gmx-users] Error of DNA topology

Dear gromacs user. i am simulating protein having DNA ,,when i applied for pdb to gmx command,it gives me error like """Residue 9 named DG of a molecule in the input file was mapped to an entry in the topology database, but the atom O5' used in that entry is not found in the input file. Perhaps

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

Thank you Justin I saw SOMNATH question and your answer about 5' PHO on 5 Jul. According that answer,  I  put PRES 5 PHO from  top_all36_na.rtf   file in merged.n.tdb  file after [5TER] section but I receive many errors like: Atom NA not found in  1GUN buiding block wile rtp and itp Atom N not

Re: [gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

Hi, That is, Tasneem's recipe will find all atoms that are in group 1 OR group 13, AND whose name is N. If Dilip just wants the atoms in group 1 AND whose name is N, then e.g. 1 & a N There are some examples in the interactive help of gmx make_ndx Mark On Tue, Jul 11, 2017 at 9:14 AM Tasneem

Re: [gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

Try this 1 | 13 & a N This will select the group 1 and 13 and all the atom having atom ID N. On Tue, Jul 11, 2017 at 12:19 PM, Dilip H N wrote: > Hello, > I am having problems during creating the indexes for atoms which have same > atom labelling for the two/three

[gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

Hello, I am having problems during creating the indexes for atoms which have same atom labelling for the two/three different molecules in the system (say nitrogen atom that is labelled as N in both the molecules). whn i gave the command:- gmx make_ndx -f md.gro -o a.ndx i am getting the prompt as