Re: [gmx-users] Using x2top and grompp

Hi, First, choose a force field that can model your system accurately. Second, use the right tool for generating a topology for that force field. Third, as Justin said, nobody can help with that unless you share the actual errors - copy and paste! But you need to grapple with the first two

Re: [gmx-users] Using x2top and grompp

> >> My goal is to get a topology.tpr and trajectory.xtc in those file formats. >> I’m starting off with .pdb, .xyz, and .gro files of an experimentally >> determined crystal structure. The crystal contains two kinds of molecules >> that interact via halogen bonding. i do not want to run

Re: [gmx-users] typeB in FEP calculations

Thank you very much for your help. I think that I finally got this straight. Cheers, Rui On 27 September 2016 at 11:26, Hannes Loeffler wrote: > On Tue, 27 Sep 2016 11:08:45 +0100 > Rui Neves wrote: > > > However, what I would like to know is:

Re: [gmx-users] Gromacs on an IBM Power8

Hi, Unless your Power8 Linux machine/kernel is configured differently from the ones I've used, thread placement with -ntomp -pinstride is quite straightforward. You can see the hardware thread to "CPU" index mapping in the log file if you compile with hwloc, under the "Hardware topology:"

Re: [gmx-users] which version would be faster?

> On 30 Sep 2016, at 16:31, Albert wrote: > > Hello: > > I've got a GPU workstation with two GPUs. I am just wondering which version > will gain a better performance? The MPI version, the thread version, or the > thread-openMP version? There are 20 threads (Intel(R)

[gmx-users] which version would be faster?

Hello: I've got a GPU workstation with two GPUs. I am just wondering which version will gain a better performance? The MPI version, the thread version, or the thread-openMP version? There are 20 threads (Intel(R) Xeon(R) CPU E5-2690 v2 @ 3.00GHz) in my workstation. I am going to run a job

Re: [gmx-users] Gromacs on an IBM Power8

Hi, You should also check out the documentation, e.g. http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html. To implement Szilard's suggestion of fewer threads per core and fewer ranks per node, for your 2-socket 24-core node, you will want something like gmx mdrun

Re: [gmx-users] Gromacs on an IBM Power8

Hi Szilard, Thank you for your detailed reply, and for the attached paper. I'm heading in the right direction -- I have upgraded to gcc v5.1 and installed fftw v3.3.5 with VSX support turned on. On the other hand I'm not that experienced with gromacs, and I would appreciate some advice on

Re: [gmx-users] Regarding constraints

On 9/30/16 9:22 AM, Apramita Chand wrote: Dear Gromacs Users, Can I use LINCS constraints instead of SHAKE algorithm while using GROMOS53a6 forcefield? Also, if I want to conduct hydrogen bond property Sure, LINCS is more stable than SHAKE. calculations, what should I set the constraint

[gmx-users] Regarding constraints

Dear Gromacs Users, Can I use LINCS constraints instead of SHAKE algorithm while using GROMOS53a6 forcefield? Also, if I want to conduct hydrogen bond property calculations, what should I set the constraint option to in my .mdp file? I'm having the constraint option as 'h-bond' now. Is it right or

Re: [gmx-users] Simulating PMMA

On 9/30/16 7:14 AM, Karel de Vries wrote: Hi Justin, Thanks for your answer; I assumed that TopolGen is not intentionally incorrect. What I meant to ask was whether it was intentionally different from what the comments in the atomtypes.atp file indicate. I thought that perhaps, based on past

Re: [gmx-users] Simulating PMMA

Hi, How did you come to decide to model with OPLS/AA? As part of that process, you should be considering whether it parameterized a quaternary carbon, e.g. by inspecting its literature, or reference implementation in BOSS. Availability of convenient tools is only one of many aspects to consider

Re: [gmx-users] Simulating PMMA

Hi Justin, Thanks for your answer; I assumed that TopolGen is not intentionally incorrect. What I meant to ask was whether it was intentionally different from what the comments in the atomtypes.atp file indicate. I thought that perhaps, based on past experience, you know that some choices work

Re: [gmx-users] parameters of GppNHp

Hi, You should add "-nc" option to your antechamber command, which specifies the net charge of your unit. You can type "antechamber -h" command to get more information. On 30 September 2016 at 16:47, Mark Abraham wrote: > Hi, > > You'll probably have better luck

Re: [gmx-users] Using x2top and grompp

On 9/30/16 5:34 AM, Devon wrote: My goal is to get a topology.tpr and trajectory.xtc in those file formats. I’m starting off with .pdb, .xyz, and .gro files of an experimentally determined crystal structure. The crystal contains two kinds of molecules that interact via halogen bonding. i do

Re: [gmx-users] Simulating PMMA

On 9/30/16 3:35 AM, Karel de Vries wrote: Hi again, I think the problem is in the force field description that I put in the aminoacids.rtp file. Like I said, I just got the output from Justin's TopolGen (V1.1) script. Upon comparison of the opls_xxx choices to the comments in the

[gmx-users] Using x2top and grompp

> My goal is to get a topology.tpr and trajectory.xtc in those file formats. > I’m starting off with .pdb, .xyz, and .gro files of an experimentally > determined crystal structure. The crystal contains two kinds of molecules > that interact via halogen bonding. i do not want to run these

Re: [gmx-users] parameters of GppNHp

Hi, You'll probably have better luck getting help with how to use AmberTools from the AmberTools documentation and the Amber mailing list. And search Google for that error message first, because it's probably been seen before. Mark On Fri, Sep 30, 2016 at 10:44 AM Anu George

Re: [gmx-users] parameters of GppNHp

Hi everyone, I am trying to do a simulation of "RAS G12V - PI 3-KINASE GAMMA COMPLEX" which has the ligands 'GNP' and Mg2+. For GNP i tried to create the topology by using antechamber giving input as GNP.pdb which was extracted from the pdb file (1he8.pdb) but it is giving the error as Error:

Re: [gmx-users] Simulating PMMA

Hi again, I think the problem is in the force field description that I put in the aminoacids.rtp file. Like I said, I just got the output from Justin's TopolGen (V1.1) script. Upon comparison of the opls_xxx choices to the comments in the atomtypes.atp file, a few strange assignments turn up. For

Re: [gmx-users] RMSD of energy minimized structure

Hi Surya, The first part ss a warning, not an error. It also says (implicitly) that if the molecules are not broken across PBC then there's nothing to worry about whatsoever. So just assert that your molecules are not split over PBC. Have a look at the trajectory. If there are frames with one