[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

[gmx-users] Concrete pull code explanation needed

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 pull_group1_name= Chain_B pull

[gmx-users] ligan minimization in vacuo

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 to create a topology for my designed drug (50 atoms)

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

Hi, I am working on a node with Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz, 16 physical core, 32 logical core and 1 GPU NVIDIA GeForce GTX 980 Ti. I am launching a series of 2 ns molecolar dynamics simulations of a system of 6 atoms. I tried diverse setting combination, but however i obtained t

Re: [gmx-users] Acetonitrile using CHARMM ff

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 around 771 g/m3 which is slightly underestimated, but close t

Re: [gmx-users] Invalid order for directive X

Hi, The output files from acpype I mean. Mark On Mon, Jul 10, 2017 at 3:59 PM Khadija Amine wrote: > Hi Mark, > > Thank you for your quick reply. > > You mean by 'the acpype files must be edited to have all the atom types in > a block before any of the molecules' all the files with GMX as I ha

[gmx-users] Invalid order for directive X

Hi Mark, Thank you for your quick reply. You mean by 'the acpype files must be edited to have all the atom types in a block before any of the molecules' all the files with GMX as I have used amberff99sb. There are many files for charmm, opls, ... In my case, I should see the following files: AC

Re: [gmx-users] Regarding terminal residue parameters (Capping)

BS”D I am trying to simulate a multichain amino acid structure. PDB ID 2BEG. I am experiencing problems with the C and N terminal residues i. e. C-ALA and N-LEU. An abnormal non-bonded interaction keeps forming between atoms C from ALA42 and N from LEU17. Do you mean from Ala42 of Chain A to

Re: [gmx-users] error in NVT run

Hello Aman, this probably means that your system is not well equilibrated. You can try a smaller time step. But I would also recommend to google the error and you will find a lot of qualified suggestions. All the best Johannes On 10.07.2017 14:33, Aman Deep wrote: hello, I was trying to

[gmx-users] error in NVT run

hello, I was trying to simulate a protein of 1200 residues, during NVT run I got error repeatedly that is: *step 11: Water molecule starting at atom 115665 can not be settled.* *Check for bad contacts and/or reduce the timestep if appropriate.* please tell me what is reason for it and how to sol

Re: [gmx-users] Can't locate state.cpt for gmx mdrun

Hi, Checkpoints continue unfinished calculations. Energy minimization generally is short, and only stops when complete, so there is no meaningful restart. Mark On Mon, 10 Jul 2017 00:13 Yonatan Zelnik wrote: > Hello Justin, > > I see now why there aren't checkpoint files being produced. I gues

Re: [gmx-users] Regarding creating topology for molecule

Hi, The rdf should be constructed from specially constructed index groups, eg from all N in a specified molecule. Don't try to involve pdb2gmx, it needs to match the names to the rtp files. Mark On Mon, 10 Jul 2017 12:06 Dilip H N wrote: > Hello, > 1] I want to simulate A and B mixtures...but

Re: [gmx-users] Invalid order for directive X

Hi, The atomtypes directive must appear early. So the acpype files must be edited to have all the atom types in a block before any of the moleculetypes. This is covered specifically at http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx Mark On Mon, 10 Jul 2017 13:35 K

[gmx-users] Invalid order for directive X

Hello, I have read the documentation and tried to solve the problem but still having the same error. Any suggestions, please? *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mai

Re: [gmx-users] Invalid order for directive X

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx -- 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)subscri

[gmx-users] Invalid order for directive X

Dear gromacs users, I have a protein with two bound ligands, GNP and ACT. For the protein I have prepared topology with amber ff96. pdb2gmx created three itp files for the two protein chains and one for CA and MG ions. Fore GNP and ACY I have generated itp files perfectly using acpype .When I

Re: [gmx-users] dihedral angles in CNT

x2top does indeed do that with graphene and CNTs. Strictly speaking, the remaining 3/4 of the dihedrals are not redundant, so ideally you should test the mechanical properties of your CNT. If the constant for the dihedral energy term came from a model, which counts all four dihedrals, I would a

Re: [gmx-users] Regarding creating topology for molecule

Hi, You can create a separate index file and feed that for your calculations. -- Regards, Nikhil Maroli -- 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/M

[gmx-users] Regarding creating topology for molecule

Hello, 1] I want to simulate A and B mixtures...but the problem is tht in both the say atoms of nitrogen's of both A and B molecules are labelled as N onlywhich during the indexing for RDF creates problems... So in the CHARMM FF .rtp file, i changed the nitrogen (of B molecule) N into N1 and t

[gmx-users] dihedral angles in CNT

Dear GROMACS users, I have used the x2top to generate a topology file for the zig-zag carbon nanotube (6,0). The pbc were applied. I noticed that the number of generated dihedral angles is just a quarter of the total number of the dihedral angles in the CNT. Actually, there are four dihedrals a