[gmx-users] amber99parmbsc1 force field

Hii all I want to use Amber99 parm bsc1 force field to simulate nucleic acid system in GROMACS 2016.3. For that I have downloaded  amber99bsc1.ff and copy the folder to gromacs software. Is this right way? Please suggest something. Is this the right force field for nucleic acids? I am attaching

Re: [gmx-users] gmx 2019 running problems

Hi, On Mon, Jan 14, 2019 at 9:06 PM Tamas Hegedus wrote: > Hi, > > I tried to install and use gmx 2019 on a single node computer with 4 GPUs. > > I think that the build was ok, but the running is... > There is only workload on 4 cores (-nt 16) and > there is no workload on the GPUs at all. >

Re: [gmx-users] gmx 2019 running problems

One other suggestion: from the PPA repository, install the Nvidia 410 driver. Your Cuda 9 install may work with the 410 driver but more likely you will need to reinstall. cuda If so, install the CUDA 10 toolkit, but DO NOT use the toolkit to install the driver when asked, it will

Re: [gmx-users] gmx 2019 running problems

Tamas I’ve the same build as you (almost… 2 gpus ) I found good results using one change : from -nt 16 to-ntomp 4 which should map the GPU’s and tasks in the same manner, but may be handled differently by mdrun. These two versions run with different efficiency on my rig. Paul >

Re: [gmx-users] ParmED

Hello, Here is my script " input.py ": # import parmed as pmd #convert prmtop and inpcrd into top and gro amber = pmd.load_file('mol_HMR.prmtop','mol_HMR.inpcrd') # amber.save('topol.top') amber.save('ions.gro') # system = pmd.load_file('topol.top') system.write('topol2.top', combine=[[0,1]]) #

[gmx-users] ParmED

Hi everybody, I am trying to convert Amber prmtop and inpcrd to gro and top with parmED, as in this post https://github.com/ParmEd/ParmEd/issues/631. But the problem is, ParmED cannot import the pmd. The error is: import command is not recognized. ParmED is working for anything else. What can be

Re: [gmx-users] how to create a index file for angle calculation

It sounds like you are measuring the angle between two planes. You then need to tell gangle that you are measuring planes (B in http://manual.gromacs.org/documentation/current/_images/sgangle.png) using -g1 plane -g2 plane, rather than the angle between three points (

[gmx-users] gmx 2019 running problems

Hi, I tried to install and use gmx 2019 on a single node computer with 4 GPUs. I think that the build was ok, but the running is... There is only workload on 4 cores (-nt 16) and there is no workload on the GPUs at all. gmx 2018 was deployed on the same computer with the same tools and

Re: [gmx-users] different nvidia-smi/gmx GPU_IDs

Thanks! On 1/14/19 7:06 AM, Mark Abraham wrote: Hi, Looks like something that NVIDIA did differently some time in the past, and unlikely to change :-( https://stackoverflow.com/questions/26123252/inconsistency-of-ids-between-nvidia-smi-l-and-cudevicegetname Mark On Sun., 13 Jan. 2019, 14:27

[gmx-users] EMBO Workshop: Visualising Biological Data (VIZBI 2019) is approaching!

* We wish you a Happy New Year 2019! This year, VIZBI returns to Germany for its 10th Anniversary - 10 years of ground-breaking talks in visualizing biological data! This year, we will have again an exciting program including a Visualization Master class to start with. The program of the EMBO

[gmx-users] Conversion CHARMM FF to Gromos54a7 FF

Dear all, I have a CHARMM all atoms force fields for a solid with limited atom types, and I want to convert them to Gromos54a7 force fields. Would you please confirm that below are the changes I should make to do so? 1. Combination rule # 2 is used in CHARMM whereas GROMOS which uses # 1, so, In

Re: [gmx-users] Results of villin headpiece with AMD 8 core

On 14.01.2019 16:32, p buscemi wrote: > Mirco, to continue the results from the 32 core AMD Ryzen 1080ti > 8.4 % of the available CPU time was lost due to load imbalance in the domain > decomposition. > Core t (s) Wall t (s) (%) > Time: 151131.597 2361.432 6400.0 > 39:21 > (ns/day) (hour/ns) >

Re: [gmx-users] Results of villin headpiece with AMD 8 core

Hi Paul, On 14.01.2019 02:48, pbuscemi wrote: > Here are the results for three runs of the million atoms DPPC > ===8 core 2700x 1080ti > == > gmx mdrun -deffnm dppc.md -nb gpu -pme gpu -ntmpi 4 -ntomp 4 -npme 1 > -gputasks > Core

Re: [gmx-users] Results of villin headpiece with AMD 8 core

Mirco, to continue the results from the 32 core AMD Ryzen 1080ti 8.4 % of the available CPU time was lost due to load imbalance in the domain decomposition. Core t (s) Wall t (s) (%) Time: 151131.597 2361.432 6400.0 39:21 (ns/day) (hour/ns) Performance: 7.318 3.280 command gmx mdrun -deffnm

Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

Hi, Yes... if 1UBQ-CG is the coordinates you want the restraints to target. Mark On Mon, Jan 14, 2019 at 3:49 PM ZHANG Cheng <272699...@qq.com> wrote: > Thank you Mark! > > > The "Protein_A.itp" is obtained by: > python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -dssp >

Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

Thank you Mark! The "Protein_A.itp" is obtained by: python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -dssp ./dssp-2.0.4-linux-amd64 -p backbone -ff martini22 So the "Protein_A.itp" has the restraints in the "1UBQ-CG.pdb". So I should use "-r 1UBQ-CG.pdb"? So the whole

Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

To add to Mark's comments, it's commonly the case that you want to apply restraints based on the starting configuration, e.g. for restraining protein positions at the beginning of a run. As the warning message says, you can pass the same file to both -c and -r for these cases. Also, you're

Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

Hi, The purpose of applying position restraints is to restrain the coordinates to a set of target coordinates. grompp now requires you to be explicit about what target you choose. You need to decide what they are, and pass the file containing them to grompp -r. Mark On Mon, Jan 14, 2019 at 3:17

Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

Thank you Mark! Sorry, I do not have a "targetcoords.gro" for the grompp. I was trying to use "gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o minimization.tpr", and the "system.top" has a line of " #include "Protein_A.itp" ", and the "Protein_A.itp" file has the restraints I

Re: [gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

Hi, On Mon, Jan 14, 2019 at 2:54 PM ZHANG Cheng <272699...@qq.com> wrote: > My backbone restraints is shown in the "Protein_A.itp" file: > > > > #ifdef POSRES > #ifndef POSRES_FC > #define POSRES_FC 1000.00 > #endif > [ position_restraints ] > 11POSRES_FCPOSRES_FCPOSRES_FC

[gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

My backbone restraints is shown in the "Protein_A.itp" file: #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FC

[gmx-users] how to create a index file for angle calculation

hi, if i want to calculate angle between two group,then the group will be in same file or in different file.because when i am using this command gmx gangle -f md-0-1-300k-pbc.xtc -n index.ndx -dt 2000 -oall angle.xvg putting the two group (1 and 2 both) in same idex file , i am getting the values

Re: [gmx-users] How To Calculate The Energy From The Coordinates Of Pdb File?

Dear Groamcs User, I would be appreciated if you guide me, how to extract pairwise energy (between residues) from the coordinates of PDB file? Since the Pdb files are already minimized, obviously, there is no needed to run energy minimization step. *Mehdi Mirzaie(PhD),* Department of Applied