Re: [gmx-users] Gromacs in UBUNTU

I am still not clear because pdb2gmx_mpi, editconf_mpi commands are working very well. Although they have mpi suffix but its working as non-MPI. Do I have to re-run with (DGMX_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF ) to get gmx solvate command ... Kindly explain. On 18 May 2015 at 20:39, Mark

Re: [gmx-users] Gromacs in UBUNTU

Hi, Use gmx_mpi solvate. You can get away with using pdb2gmx_mpi in GROMACS 5 just like old GROMACS versions only because those are magically transformed into things like gmx_mpi pdb2gmx, to provide a year of backwards compatibility. But providing backwards compatibility for a new name was not

Re: [gmx-users] Gromacs in UBUNTU

Hi, These are not the installation steps you said you followed. Those previous instructions were for a non-MPI build. You've done an MPI build, which explains all your problems. Please be precise ;-) On Mon, May 18, 2015 at 3:55 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: definitely

Re: [gmx-users] position resrtraints

Dear Justin, thanka 4 ur prompt reply. I checked that there was another issue. I didnot modify the aminoacids.rtp file in order to incorporate the new graphene.pdb atom types according to the force field. It appears to me that the correct interaction is not arsising because the

[gmx-users] Best way/utility to convert .xtc to .dcd

Hello All, What is the best way/utility available to convert GROMACS .xtc to a CHARMM .dcd. I have tried CATDCD but I am not getting a desired outcome. Kindly help. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Implementing an angle-dependent potential

Hi all, I am trying to add hydrogen bonds to a coarse grained protein model by Ali Ghavami. The model has one bead per amino acid placed at each C-alpha. The model has bending and torsion potentials, and also includes non-bonded interactions like hydrophobicity and electrostatic interactions.

Re: [gmx-users] Gromacs in UBUNTU

Hi, Did you go and read the webpage that is suggested by the rest of that message? Mark On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been

Re: [gmx-users] Gromacs in UBUNTU

definitely yes.. Then only I came to know about this gmx solvant... else How could I? my installation steps are follwoing - -- # tar xfz gromacs-5.0.4.tar.gz # cd gromacs-5.0.4 # mkdir build # cd build #sudo CMAKE_PREFIX_PATH=/soft/fftw333/lib cmake ..

Re: [gmx-users] first residue in chains warning issue

On 5/18/15 7:53 AM, Ming Tang wrote: Hi Justin, Do you mean options for bonds or something like fix and pull atoms? From the error... Maybe you forgot to change the constraints mdp option. -Justin -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] first residue in chains warning issue

Hi Justin, Do you mean options for bonds or something like fix and pull atoms? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 18 May 2015 9:44 PM To:

Re: [gmx-users] energy minimization problem

Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf

Re: [gmx-users] Gromacs in UBUNTU

Hi, You may need to give your normal user account read permission to that directory. gmx solvant doesn't exist, of course, but I assume that was a typo! :-) Mark On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Dear all I followed the same steps to install

Re: [gmx-users] warter freeze into ice when cutoff-scheme=Verlet and coulombtype = cut-off

Hi, That behaviour might depend on what your starting configuration is, e.g. what group MOL has frozen coordinates. But cut-off is anyway a ~useless model for condensed phase of atoms with partial charges, so understanding the issue hasn't got much value. Mark On Mon, May 18, 2015 at 3:58 AM

Re: [gmx-users] energy minimization problem

Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for

Re: [gmx-users] energy minimization problem

Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated

[gmx-users] normal mode analysis and system size ...

hi , I've been trying to perform a nromal mode analysis using (after a thorough energy minimization of my system) prompt mdrun_d -v -s nm.tpr  -o nm.trr -mtx nm.mtx[...] Maximum force: 8.56366e+00 The force is probably not small enough to ensure that you are at a minimum. Be aware that negative

Re: [gmx-users] energy minimization problem

Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed

[gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions. Information for gromacs 5 is here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM However,

[gmx-users] Protein-Ligand complex Implicit simulation

Hello Everyone, I am trying to do protein-ligand complex simulation with implicit solvent parameters using gromacs. As, ligand parameters are not present in gbsa.itp, I added all the possible atomtypes and their van der wall radii from gaff ff and also managed to get get the HCT paremeters.

[gmx-users] question

Dear Mark I installed the newest version of cmake (3.2.2). After using cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)

Re: [gmx-users] question

On Mon, May 18, 2015 at 9:15 PM Andrew Bostick andrew.bosti...@gmail.com wrote: Dear Mark I installed the newest version of cmake (3.2.2). After using cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA

Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

Dear Justin: Thank you for the suggestion. I don't use gromacs 5 because of things like this: http://redmine.gromacs.org/issues/1603 that tend to pop up early in a release series. Until I needed to run charmm simulations, I use 4.6.7 because it works and I am confident in it. But your

Re: [gmx-users] Gromacs in UBUNTU

Thanks Marks and really sorry for all trouble because of my stupid understanding... On 18 May 2015 at 20:58, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Use gmx_mpi solvate. You can get away with using pdb2gmx_mpi in GROMACS 5 just like old GROMACS versions only because those are

[gmx-users] Gromacs Error

Dear All, i'm geting below error while subjecting my system (Protein-ligand) for equlibriation in nvt.mdp file mgmibt@mgmibt:~/gromacs-4.5.3/recent/files$ grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr :-)  G  R  O  M  A  C  S  (-:    

Re: [gmx-users] position resrtraints

On 5/18/15 8:47 AM, soumadwip ghosh wrote: Dear Justin, thanka 4 ur prompt reply. I checked that there was another issue. I didnot modify the aminoacids.rtp file in order to incorporate the new graphene.pdb atom types according to the force field. It appears to me that the

Re: [gmx-users] Protein-Ligand complex Implicit simulation

On 5/18/15 3:35 PM, sunita gupta wrote: Hello Everyone, I am trying to do protein-ligand complex simulation with implicit solvent parameters using gromacs. As, ligand parameters are not present in gbsa.itp, I added all the possible atomtypes and their van der wall radii from gaff ff and also

Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

On 5/18/15 2:21 PM, Christopher Neale wrote: Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions. Information for gromacs 5 is here:

Re: [gmx-users] RDF

Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O is a reference atom during

[gmx-users] Force field parameterization for PAMAM dendrimers

Dear all, I want to perform MD simuations on PAMAM dendrimers, but unfortunately this molecule has not been defined in any of the GROMACS force fields. Therefore, I should parameterize the force field for my purpose. How should I do this procedure? (It is mentionable that I read the

[gmx-users] increasing simulation time via temperature rising

Hi all I'm studying effect of temperature on incredibly stable protein. I've started simulating at 300K then, 400K and 500K. 30ns simulating takes about 4days for these three temperature in a same system. when I want to run 30ns simulation at 600K, it will take more than 20 days does rising

Re: [gmx-users] increasing simulation time via temperature rising

Hi Nazli, No, that's not related to temperature. Otherwise you'd probably see a trend. I guess with the 600K simulation you have another process that interferes and eats CPU. Mind that a simulation running on four/eight cores will be affected significantly by anything that uses a considerable

Re: [gmx-users] question

Hi, I think you just hit a moment when the server was not available. Please try again. Mark On Sun, 17 May 2015 16:44 Andrew Bostick andrew.bosti...@gmail.com wrote: Dear Justin Thanks for your answer. At first, I installed cmake 2.8.8 on centOS, by following commands: ./bootstrap;

Re: [gmx-users] energy minimization problem

Hi Tsjerk, My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used is here: python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22 -collagen editconf -f hyp-CG.pdb -c -d 1 -o

Re: [gmx-users] energy minimization problem

Hi Tsjerk, I used the original structure generated by sabbac. My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used is here: python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22

Re: [gmx-users] Force field parameterization for PAMAM dendrimers

Dear Farideh, We have recently published an article on PAMAM dendrimers. We used oplsaa forcefield. You can access the paper at http://pubs.rsc.org/en/content/articlelanding/2015/sm/c5sm00854a. Hope it helps. Chandan On Mon, May 18, 2015 at 12:58 PM, faride badalkhani

Re: [gmx-users] energy minimization problem

Besides, the martini.itp does not contain moleculetype CL, so I edit it like this: [ moleculetype ] ; molname nrexcl CL1 [ atoms ] ;id typeresnr residu atomcgnrcharge 1 P4 1 CL CL 1 -1 Please help to have a look. I do

Re: [gmx-users] increasing simulation time via temperature rising

Hi Nazli, Also, I doubt simulations beyond 400 K make any sense: not only such conditions are implausible for a protein to exist in, but, as far as I know, the force fields are not parametrized to work so far beyond room temperature. cheers, M. 2015-05-18 9:05 GMT+02:00 Tsjerk Wassenaar

Re: [gmx-users] energy minimization problem

Hi Tsjerk, This protein has a total charge of 35e, and I added 35 CL to balance the system. Is there any difference between adding CL and not adding CL? Thank you. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] Gromacs in UBUNTU

Hi actually all other commands are working fine. only when I am runing: -- g@chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o solv.pdb No command 'gmx' found, did you mean: Command 'gm' from package 'graphicsmagick' (universe) Command 'gcx'

Re: [gmx-users] Gromacs in UBUNTU

Hi, What other commands are working? Please be specific, we don't have time to spend on guesses :-) Mark On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa srajkhow...@gmail.com wrote: Hi actually all other commands are working fine. only when I am runing: --

Re: [gmx-users] Gromacs in UBUNTU

sorry.. I mean pdb2gmx, editconf, genion, grompp and mdrun even it has genbox but it says This tool has been removed from Gromacs 5.0. On 18 May 2015 at 15:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What other commands are working? Please be specific, we don't have time to

[gmx-users] position rstraints

Hi all, I am trying to see the unzipping of double stranded DNA on the surface of graphene nanosheets. I am using GROMOS 53a5 force field and I obtained a graphene sheet from ATB software. i obtained both the .itp as well as the PDB from that site. Now, I proceeded for molecular dynamics

Re: [gmx-users] first residue in chains warning issue

Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 1.0e-03 ps.

Re: [gmx-users] RDF

On 5/18/15 2:55 AM, mah maz wrote: Hi Justin The fact is I want to calculate water density in the system. If I select group1: oxygen and group2: oxygen, g_rdf command gives me very large numbers. Is it the number of atoms that should be changed to g/cm3? Besides, what does it calculate, each O

Re: [gmx-users] first residue in chains warning issue

On 5/18/15 7:39 AM, Ming Tang wrote: Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10

Re: [gmx-users] position rstraints

On 5/18/15 6:55 AM, soumadwip ghosh wrote: Hi all, I am trying to see the unzipping of double stranded DNA on the surface of graphene nanosheets. I am using GROMOS 53a5 force field and I obtained a graphene sheet from ATB software. i obtained both the .itp as well as the PDB from that