Re: [gmx-users] g_energy definition

On 7/23/14, 11:05 PM, Andy Chao wrote: Dear GROMACS USERS: Thanks a lot for your supports and help! I would like to ask more questions related to the output (*.xvg) of the command g_energy. 1. GROMACS computes the potential energy of an ionic liquid to be negative beyond a specific time.

[gmx-users] Fwd: Obtaining Positive Energy Values for Both Potential and Total Energies

Hi, Please leave the discussion on the list. Others may wish to contribute or learn from it! :-) -- Forwarded message -- From: Yip Yew Mun yipy0...@gmail.com Date: Thu, Jul 24, 2014 at 5:16 AM Subject: Re: [gmx-users] Obtaining Positive Energy Values for Both Potential and Total

Re: [gmx-users] Angle group

I tried using g_angle with an index file defining the three atoms that make up the bond as Group12 ( O1_C1_C4) has 960 elements. I get: Group 0 ( System) has 27396 elements Group 1 ( Other) has 6768 elements Group 2 ( GL4b) has 352 elements

[gmx-users] Fw:Normal Mode Analysis

Dear all, I wonder if there is anywhere I can know the details of mdp files used for normal mode analysis. I understand from the maunal that it needs steepest descent, conjugate gradient, l-bfgs, nm in md options consecutively, but I am not sure about other parameters set in these

Re: [gmx-users] Angle group

On 7/24/14, 8:55 AM, Cyrus Djahedi wrote: I tried using g_angle with an index file defining the three atoms that make up the bond as Group12 ( O1_C1_C4) has 960 elements. I get: Group 0 ( System) has 27396 elements Group 1 ( Other) has 6768 elements

[gmx-users] continuation run segmentation fault

Dear all I am having some trouble continuing some runs with Gromacs 4.5.5 in our local cluster. Surprisingly, the simulations run smoothly in the same number of nodes and cores before in the same system. And even more surprisingly if I reduce the number of nodes to 1 with its 12 processors, then

Re: [gmx-users] Error in system_inflate.gro coordinates does not match

hello everyone thank you justin i did the same till minimization without the ligand it is in the lipid and center but i edit the box size arbitrary i used x and y axis as present in popc but in z axis used 10.0 so there is overlapping of protein and lipid i think this can create problem help

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 123, Issue 124: reply to message 1

Thanks for the reply! I actually managed to solve this issue. I was building the super cell with Mercury, the Cambridge Crystallographic Database software, but I was not aware of connectivity issues that appeared when I built the crystal with fragments of molecules. It was solved easily with a

Re: [gmx-users] Issues using tabulated potentials for coarse-grained simulation

Thanks for the response. I have looked at two particles in NVT with v-rescale/large box and there was nothing wrong with the intra/inter molecular interaction energies. I also switched rvdw-switch to rvdw without observing any difference. I ran into a similar issue when using this force field in

[gmx-users] Gromacs performance on virtual servers

Dear Gromacs Users, My former university is focusing on cloud computing instead of physical servers, so research groups are now expected to buy virtual servers from the university coloud instead of buying their own clusters. The current setup employs Xeon E7- 2870 servers and there is an

[gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

Dear all, Please help me out. Thanks in advance. I had written some analyzing codes, which can be easily compiled under Gromacs 4.5.5. Since I switched to GMX 5.0 weeks ago, I want to re-compile them under GMX5.0. But the GMX5.0 seems quite different from GMX4.5.5. Anyone can help me? Thanks

Re: [gmx-users] Issues using tabulated potentials for coarse-grained simulation

Sounds to me like the model is broken, if you can only observe sensible things in the presence of heat to flow between cations and anions via the thermal reservoir. Does NVE work? Mark On Thu, Jul 24, 2014 at 10:27 PM, Brian Yoo brian.s.yoo...@nd.edu wrote: Thanks for the response. I have

[gmx-users] time accounting in log file with GPU

Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My grompp.mdp file is attached below. However, in the time accounting table in the md.log, I

Re: [gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

On Thu, Jul 24, 2014 at 11:47 PM, qiaobf qia...@gmail.com wrote: Dear all, Please help me out. Thanks in advance. I had written some analyzing codes, which can be easily compiled under Gromacs 4.5.5. Since I switched to GMX 5.0 weeks ago, I want to re-compile them under GMX5.0. But the

Re: [gmx-users] continuation run segmentation fault

Hi, There is a certain version of MPI that caused a lot of headache until we realized that it is buggy. I'm not entirely sure what version was it, but I suspect it was the 1.4.3 shipped as default on Ubuntu 12.04 server. I suggest that you try: - using a different MPI version; - using a single

Re: [gmx-users] time accounting in log file with GPU

On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am running a benchmark test with the GPU. The system consists of simple LJ atoms. And I am running only very basic simulation with NVE ensemble and not writing any trajectories or energy values. My

Re: [gmx-users] Gromacs performance on virtual servers

Hi, Except for huge simulation systems, GROMACS performance past a single node is dominated by network latency, so unless you can extract a promise that any multi-node runs will have Infiniband-quality latency (because the nodes are physically in the same room, and on Infiniband) you can forget

Re: [gmx-users] time accounting in log file with GPU

Thanks Mark. -noconfout option helps. -- Sikandar On Thu, Jul 24, 2014 at 3:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I am running a benchmark test with the GPU. The system consists of simple

Re: [gmx-users] time accounting in log file with GPU

On Fri, Jul 25, 2014 at 12:48 AM, Sikandar Mashayak symasha...@gmail.com wrote: Thanks Mark. -noconfout option helps. For benchmarking purposes, additionally to -noconfout I suggest also using: * -resethway or -resetstep: to exclude initialization and load-balancing at the beginning of the run

Re: [gmx-users] Gromacs performance on virtual servers

On Fri, Jul 25, 2014 at 1:51 AM, Szilárd Páll pall.szil...@gmail.com wrote: Hi In general, virtualization will always have an overhead, but if done well, the performance should be close to that of bare metal. However, for GROMACS the ideal scenario is exclusive host access (including

Re: [gmx-users] Gromacs performance on virtual servers

Hi In general, virtualization will always have an overhead, but if done well, the performance should be close to that of bare metal. However, for GROMACS the ideal scenario is exclusive host access (including hypervisor) and thread affinities which will both depend on the hypervisor

Re: [gmx-users] Error in system_inflate.gro coordinates does not match

On 7/24/14, 11:57 AM, RINU KHATTRI wrote: hello everyone thank you justin i did the same till minimization without the ligand it is in the lipid and center but i edit the box size arbitrary i used x and y axis as present in popc but in z axis used 10.0 so there is overlapping of protein

Re: [gmx-users] Lennard-Jones potential not matching with published data

On 7/24/14, 4:30 PM, Elton Carvalho wrote: On Wed, Jul 23, 2014 at 3:40 PM, ibrahim khalil ibrahim.khalil.c...@gmail.com wrote: In my simulation, my results are about half (not exactly half but around half) of the published data. I am stuck here for like a month and cannot find my mistakes.

Re: [gmx-users] Lennard-Jones potential not matching with published data

On Thu, Jul 24, 2014 at 10:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/24/14, 4:30 PM, Elton Carvalho wrote: I've been there before. Check which Lennard-Jones function was used to publish the data to which you are comparing. There are some nomenclature differences regarding sigma.

[gmx-users] Re grompp and mdrun output files

Hi GROMACS users, I typed the command grompp -f md300.mdp -c equi_new.gro -n dex.ndx -p topol.top -maxwarn 1 -o md300.tpr then this command mdrun -v -deffnm md300 So, I was expecting that the md300.gro output file will be same to the last frame when I load the md300.xtc on the equi_new.gro