[gmx-users] (no subject)

Dear user, I have generated my final protein.pdb file by using trjconv command from .xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening it for docking purpose my computer is freezing. Now how can I reduce my pdb file size from GB to MB for using it properly. please help me

[gmx-users] warning 1-4 interaction in QMMM simulation

Dear gromacs users i was trying to perform micro-iterative QMMM optimization using gromacs/orca interface... in mdp file, i set bOpt = yes, then i got a warning like this: "Warning: 1-4 interaction between 3 and 6 at distance 3.565 which is larger than the 1-4 table size 2.000 nm, These are

Re: [gmx-users] md-vv integrator on gromacs 4.5.5

Thank you for your suggestion. I checked the release notes and saw the bug reported in gromacs 4.6. Thanks again, Yao > 在 2016年5月13日，17:51，Justin Lemkul 写道： > > > >> On 5/13/16 5:49 PM, LiYao wrote: >> Hi gromacs users, >> >> I tried to run md-vv along with nose-hoover

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

thanks a lot for your fast response. I have tried it, and it failed. I ask in this forum just to make sure. However, there was something in my cluster that probably make it failed. I'll handle it first and then retry to restart again. Regards, Husen On Sat, May 14, 2016 at 7:58 AM, Justin

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

On 5/13/16 8:53 PM, Husen R wrote: Dear all Does simulation able to be restarted from checkpoint file with fewer nodes ? let's say, at the first time, I run simulation with 3 nodes. At running time, one of those nodes is crashed and the simulation is terminated. I want to restart that

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

I use Gromacs-5.1.2 and SLURM-15.08.10 as a resource manager. On Sat, May 14, 2016 at 7:53 AM, Husen R wrote: > Dear all > > Does simulation able to be restarted from checkpoint file with fewer nodes > ? > let's say, at the first time, I run simulation with 3 nodes. At running

[gmx-users] Restart simulation from checkpoint file with fewer nodes

Dear all Does simulation able to be restarted from checkpoint file with fewer nodes ? let's say, at the first time, I run simulation with 3 nodes. At running time, one of those nodes is crashed and the simulation is terminated. I want to restart that simulation immadiately based on checkpoint

Re: [gmx-users] md-vv integrator on gromacs 4.5.5

On 5/13/16 5:49 PM, LiYao wrote: Hi gromacs users, I tried to run md-vv along with nose-hoover thermostat on gromaces 4.5.5 but it resulted in a temperature 300 K higher than the reference temperature. However, I run the same simulation on gromacs 4.6.5 and it worked well. Has anyone

[gmx-users] md-vv integrator on gromacs 4.5.5

Hi gromacs users, I tried to run md-vv along with nose-hoover thermostat on gromaces 4.5.5 but it resulted in a temperature 300 K higher than the reference temperature. However, I run the same simulation on gromacs 4.6.5 and it worked well. Has anyone encountered the same problem? Can I still

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

Hi Antara, What commands did you use? At least make sure you add -rdd 1.6 to the command line of mdrun, because the default value is too small for coarse grain simulations. Cheers, Tsjerk On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar wrote: > Dear users, > > I am

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

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

Hi, Several things will make it easier to help - particularly your GROMACS versions and how you ran mdrun. See also http://www.gromacs.org/Support Mark On Fri, May 13, 2016 at 7:42 PM Antara mazumdar wrote: > Dear gromacs users, > > I am trying to run a coarse grained

[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

Re: [gmx-users] pdb2gmx error after switching force fields

On 5/13/16 11:04 AM, Irem Altan wrote: Hi, Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually using Gromacs 5.1.2. Not sure how that's possible. It should have been fixed prior to the release of 5.1.1. -Justin Best, Irem On May 13, 2016, at 10:52 AM,

Re: [gmx-users] pdb2gmx error after switching force fields

Hi, Thanks for the quick reply. Erasing the dihedral with CB worked. I’m actually using Gromacs 5.1.2. Best, Irem > On May 13, 2016, at 10:52 AM, Justin Lemkul wrote: > > > > On 5/13/16 10:49 AM, Irem Altan wrote: >> Hi, >> >> I have a .pdb file that I’ve used in

Re: [gmx-users] Hydrophobic interaction analysis

On 5/13/16 8:23 AM, Nikhil Maroli wrote: We can analyse hydrogen bond numbers, what about total hydrogen bond energy between two molecules over time like that in case of hydrophobic There is no such energy term. A hydrogen bond is largely electrostatic, though, so short-range Coulombic

Re: [gmx-users] pdb2gmx error after switching force fields

On 5/13/16 10:49 AM, Irem Altan wrote: Hi, I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning: WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped to an

[gmx-users] pdb2gmx error after switching force fields

Hi, I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning: WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom

Re: [gmx-users] Gromacs installation.

With that amount of information it'll be hard for anyone to diagnose your issue -- unless someone else ran into the same problem. If you want help you need to i) try hard ii) try harder iii) describe what you tried and you failed. -- Szilárd On Fri, May 13, 2016 at 12:53 PM, Elsaid Younes

Re: [gmx-users] Hydrophobic interaction analysis

We can analyse hydrogen bond numbers, what about total hydrogen bond energy between two molecules over time like that in case of hydrophobic interaction,is there any possibility to know the energy involved in the process -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Re. Generating topology for Tetrahydrofolate within CHARMM ff

penalties were not good at all (> 50 and between 10 and 50)! How can I fix the file? 'https://cgenff.paramchem.org/initguess/#20160513/THF_zinc_4228237.str' You'll need to manually parametrize/refine anything that has bad penalties. Spend some time with the CGenFF paper and tutorial: h

Re: [gmx-users] Hydrophobic interaction analysis

hi Its hydrophobic effect, Nikhil. And you can make index of hydrophobic groups in your protein, then calculate distance between them. On Thu, May 12, 2016 at 11:03 PM, Nikhil Maroli wrote: > Dear all, > > is there any option in gromacs to study the hydrophobic interaction

[gmx-users] Gromacs installation.

Hi all, I have installed gromacs like the quick and dirty installation. I have a 16.04 version of ubuntu. I can not start it. I used to do the same procedure in ubuntu 15.10, and it worked fine. /Elsaid -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Re. Generating topology for Tetrahydrofolate within CHARMM ff

10 and 50)! How can I fix the file? 'https://cgenff.paramchem.org/initguess/#20160513/THF_zinc_4228237.str' Thank you very much for your help. Zeineb. -- Gromacs Us

Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

/initguess/#20160513/THF_zinc_4228237.str' in a another post and I just added a comment)). Thank you very much for your help. Zeineb. -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Making separate topology file for QM atoms (bharat gupta)

You need to make one topology for your protein that includes all atoms that you want to treat with QM. If your QM region includes part of the protein and the ligand, you can most easily make one topology with the -merge option of pdb2gmx. Gerrit Dear Gromacs Users, I am interested to know how

Re: [gmx-users] REMD error

Hi, If you've configured with GMX_MPI, then the resulting GROMACS binary is called gmx_mpi, so mpirun -np X gmx_mpi mdrun -multi ... Mark On Fri, May 13, 2016 at 10:09 AM YanhuaOuyang <15901283...@163.com> wrote: > Hi, > I have installed the openmpi 1.10, and I can run mpirun. When I installed

Re: [gmx-users] REMD error

Hi, I have installed the openmpi 1.10, and I can run mpirun. When I installed grimaces 5.1, I configured -DGMX_MPI=on. And the error still happens . > 在 2016年5月13日，下午3:59，Mark Abraham 写道： > > Hi, > > Yes. Exactly as the error message says, you need to compile GROMACS

Re: [gmx-users] REMD error

Hi, Yes. Exactly as the error message says, you need to compile GROMACS differently, with real MPI support. See http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations Mark On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:

[gmx-users] REMD error

Hi, I am running a REMD of a protein, when I submit "gmx mdrun -s md_0_${i}.tpr -multi 46 -replex 1000 -reseed -1", it fails as the below Fatal error: mdrun -multi or -multidir are not supported with the thread-MPI library. Please compile GROMACS with a proper external MPI library. I have

Re: [gmx-users] REMD on more than one node

Hi, You'll need to choose a replica setup that naturally fits on your available hardware. Number of nodes * number of cores per node must equal number of replicas * number of cores per replica. See also

[gmx-users] PME and particle insertion

Dear all, I see that issues concerning PME and particle insertions have been discussed before, and some issues were apparently resolved for the latest (5.1.2) version. However, I have noticed a strange thing when using TPI for inserting (tip3p) water in liquid water at 300 K and 1 atm; the

[gmx-users] Regarding Dynamic cross correlation map analysis

Hi,I am working on MD studies of Protein-DNA complex.I get trajectories from gromacs version 5.1 . NowI want to form dynamic cross correlation mapfrom thesetrajectories.Please let me know which software can read .trr file and I can use to plotDynamic cross correlation map.I have read VMD