Re: [gmx-users] Missing terminal cap group

Dear Justin, Thanks for the reply. I just had a recheck of Gromacs Charmm36ff provided in Grocmacs website ( http://www.gromacs.org/Downloads/User_contributions/Force_fields). Unfortunately ACE group is missing in the .rtp file and also, in the .n.tdb file. But, it is present in the Chramm27ff,

Re: [gmx-users] Topology for ready-made membrane protein system

Dear Justin, Do I need to add lipid topology manually, if I use Charmm36 force filed that have protein and lipid parameters together? Thanks Anu On Fri, Jul 3, 2015 at 4:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/3/15 7:56 AM, anu chandra wrote: Dear Gromacs users, I am working

[gmx-users] Installation problem

Hi, I want to install gromacs 5.0.5 but after issuing this command: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON I encounter the folloeing error: Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz CMake Error at tests/CMakeLists.txt:57 (message):

Re: [gmx-users] Installation problem

Hi, The real problem description is at the end. You are doing the download with a cmake that relies on curl that relies on libssl and that doesn't support the boring standard https protocol. Perhaps your operating system is too old to be useful. You can bypass this and get the tests yourself,

Re: [gmx-users] Topology for ready-made membrane protein system

On 7/6/15 7:05 AM, anu chandra wrote: Dear Justin, Do I need to add lipid topology manually, if I use Charmm36 force filed that have protein and lipid parameters together? You always need a topology for any molecule in the system. -Justin Thanks Anu On Fri, Jul 3, 2015 at 4:47 PM,

Re: [gmx-users] Topology for ready-made membrane protein system

Hi, You need a topology for each moleculetype, and parameters for the interactions they require. These are separate issues. Mark On Mon, 6 Jul 2015 13:05 anu chandra anu80...@gmail.com wrote: Dear Justin, Do I need to add lipid topology manually, if I use Charmm36 force filed that have

[gmx-users] GPU/CPU load imbalance

I have 3x GTX 970 for 1x Intel i7-5820K with X99-E WS motherboard to remove PCIe limitations. So I have 4 threads/gpu and I face load imbalances. I am wondering if it will be a good idea to use reaction-field instead of PME in order to reduce the processor load (It would be less accurate). Let

Re: [gmx-users] Missing terminal cap group

On 7/6/15 6:59 AM, anu chandra wrote: Dear Justin, Thanks for the reply. I just had a recheck of Gromacs Charmm36ff provided in Grocmacs website ( http://www.gromacs.org/Downloads/User_contributions/Force_fields). Unfortunately ACE group is missing in the .rtp file and also, in the .n.tdb

[gmx-users] Gromcas tools listing with 'gmx'

Dear Gromcas users, I have installed latest version of Gromcas and while using I am adding 'gmx' prior the all the Gromacs tools ( for eg, pdb2gmx). Unfortunately, the 'TAB' key failed to list the possible commands if I use 'gmx' prior to any Gromacs tools.This leaves me each time to remember

[gmx-users] GROMACS 5.1 release candidate available

Hi GROMACS users, The first release candidate of GROMACS 5.1 is now available! We are making this available to you to get a near-final taste of how GROMACS 5.1 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the

Re: [gmx-users] Gromcas tools listing with 'gmx'

This is to confirm that I also get an embarrassment of choices on my local box, but empty on the cluster nodes. Otherwise, everything works the same way on both. Not that I care about the listing, but yeah. :) Alex On Mon, Jul 6, 2015 at 1:14 PM, Mark Abraham mark.j.abra...@gmail.com wrote:

Re: [gmx-users] GPU gromacs

Of course you can, but with such a low-end mobile GPU you may not even gain performance from offloading computation from the CPU and additionally you may have issues with cooling too. You can simply try comparing performance with -nb cpu and -nb gpu to see if using the GPU improves performance at

Re: [gmx-users] GPU/CPU load imbalance

What kind of load imbalance? I assume you are referring to CPU-GPU imbalance as your runs are CPU-bound. In that case the only thing that helps is either porting code to CUDA or a faster CPU. Reaction field electrostatics will help too in getting better performance in CPU-bound runs, but beware

Re: [gmx-users] Gromcas tools listing with 'gmx'

Hi, Having sourced GMXRC in my bash shell, typing gmx, space, TAB gives me an embarassment of choices. Does it not for you? Mark On Mon, Jul 6, 2015 at 5:36 PM anu chandra anu80...@gmail.com wrote: Dear Gromcas users, I have installed latest version of Gromcas and while using I am adding

Re: [gmx-users] g_clustsize

On 06/07/15 06:05, V.V.Chaban wrote: The sum of these probabilities is never the same. It is confusing. If no clusters exist (all particles are lone) then the sum of probabilities equals the sum of all particles. If clusters exist, the sum is different and it is unclear how it is derived. If

[gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)

Hello, I'm attempting to simulate ice ih in a triclinic box with a rigid tip4p water model. As the subject says, I get warnings (almost immediately) that shake failed to converge in 1000 steps and then eventually a segmentation fault. Gromacs documentation suggests that this is a result of my

[gmx-users] question

Dear gromacs users I am doing md simulation of protein-ligand using 5.0 version of gromacs. I want to use prodrg server for my ligand. Based on Justin's opinion, the charges should be modified. The structure of my ligand is in a way that I can't use charge of the functional groups being in

[gmx-users] Building gromacs on CRAY XC40

Dear Gromacs users, I am trying to build gromacs on our latest supercomputer CRAY XC40, but I am unable to do so because of lack of administrator privileges and different programming environment, w.r.t. my previous experience on tyrone supercomputers. I continuously get errors regarding something

[gmx-users] How to justify when the trajectory reached equilibrium

Hi, I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium... Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and kept stable after that. Could I justify that the system reached equilibrium at 12 ns? Are there any

Re: [gmx-users] Building gromacs on CRAY XC40

Hi, your not saying what version you are trying to install. Assuming 5.0.5 it should just work with cmake -DGMX_BUILD_SHARED_EXE=off .. Make sure to select GCC or ICC as compiler with a command such as (might be different on your machine) module swap PrgEnv-pgi PrgEnv-gnu If it still doesn't

Re: [gmx-users] Energy contribution of individual residues

IIRC, you do not need to redo the whole run. You can specify the new energygrps in the mdp file and use mdrun -rerun to re-process the results you already have. Check the manual for the exact syntax. Hope this helps Victor 2015-07-02 23:50 GMT-05:00 Dr. Seema Mishra seema_...@yahoo.com:

[gmx-users] monitor the size of the computational box

Dear all, I would like to ask what is the best way to monitor the size of the computational box (i.e. the volume) during a simulation. I know that it must stay constant during the simulation but, in my case, it seems that it doesn't. There is an error poping up when I try to use the gmx hbond

Re: [gmx-users] monitor the size of the computational box

On 7/6/15 11:15 AM, Giannis Gl wrote: Dear all, I would like to ask what is the best way to monitor the size of the computational box (i.e. the volume) during a simulation. I know that it must stay constant during the simulation but, in my case, it seems that it doesn't. The box is only