Re: [gmx-users] Volume of active site

Thanks Dr Gaurav , I will give a try in there . Regards, Raja On Jun 5, 2015 11:02 AM, Gaurav Goel gauravgoel...@gmail.com wrote: CASTp might prove useful. http://sts.bioe.uic.edu/castp/ -g On Thu, Jun 4, 2015 at 8:31 PM, Raj D gromacs.fo...@gmail.com wrote: Thanks Dr Erick . On Jun

[gmx-users] il -simulation -reg

Dear users, i am working in the ionic liquids simulation. i am having both anion and cation itp file. i have two query reagrding the simulation. 1. how did the two itp file be combined? 2. how to create the force filed itp files for this molecules? thanks in advances with regards uma -- Gromacs

Re: [gmx-users] .trr file

Hi, Put the command line nstout, nstout (Output control-chapter 5-Gromacs manual) on your mdp file. Phan Vy 2015-06-05 13:36 GMT+09:00 Swapnil Kate swapnilk...@rocketmail.com: hello, These are my files, in EM step it is generating .trr file and in NVT and NPT it coulden't. I am still

[gmx-users] g_covar

Hi, I need help please. I am calculating entropy of a single water in water solution. So I did a 10 ns NPT. Then I run g_covar -f NPT.xtc -s NPT.tpr -o -l -av -v and g_anaeig_d -v eigenvec.trr -entropy -eig eigenval.xvg I have two questions. 1- In the g_covar it asks to select group,

Re: [gmx-users] Problem in energy minimization

Dear Justin, I have tried to change the box size, make it smaller a little, solvate again and then, the error is resolved. Actually, I don't understand the reason. especially, I have no idea about the impossible geometry as you mentioned. Can you give me a little explanation? Thank you so much.

Re: [gmx-users] Problem in energy minimization

Hi Jin, Can you give the protocol you used in commands? And what are the box dimensions and how many solvent molecules were added? Cheers, Tsjerk On Jun 5, 2015 08:30, Jin J.C jcjin.hcmut@gmail.com wrote: Dear Justin, I have tried to change the box size, make it smaller a little, solvate

Re: [gmx-users] Problem in energy minimization

Dear Justin, My protocol is simply like this: 1. Prepare the system of protein embedded in a equilibrated pure DOPC bilayer. 2. Make a rectangular box gmx editconf -f protein-mem.gro -o protein-mem-box.gro -box 14.6 14.6 16.3 -center 7.3 7.3 8.15 3. solvate gmx solvate -cp protein-mem-box.gro

[gmx-users] CLAYFF in GROMACS

Dear all, I would like to simulate clay mineral with Gromacs and use the CLAYFF force filed. How should I do knowing that the parameters are published ? Or anyone has already entered those parameters in the Gromacs format ? Thanks in advance for your answer, Fabienne. -- Gromacs

Re: [gmx-users] temperature problem

Hi Justin... Yes I agree my system is behaving absurdly . But I am wondering why !!I have done minimization without any error ..here is the result ... Steepest Descents converged to Fmax 1000 in 1004 steps Potential Energy = -9.6667906e+05 Maximum force = 9.7920349e+02 on atom 796 Norm of

Re: [gmx-users] nvt equilibration; error

On Jun 4, 2015, at 11:15 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Date: Thu, 4 Jun 2015 20:15:54 -0700 From: marzieh dehghan dehghanmarz...@gmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] nvt

[gmx-users] energy between different groups

Hi, I simulate liquid water 1397 molecules with specifying two groups with index file; 1 molecule and rest of the molecules 1396. When I obtain average LJ energy per molecule for whole system (with -nmol), I get 16 kJ/mol, but when I obtain it from interaction between groups,

[gmx-users] GPU acceleration

Hi all, We're about to start a bit of a toy project to test GPU-accelerated GMX. What I have here is my old workstation (Dell Precision T3500: Quad-core Xeon W3530 @ 2.8 GHz, 12 gigs of RAM) running Linux Mint 17.1. The plan is to get something like GeForce GTX 750 (

Re: [gmx-users] temperature problem

On 6/5/15 8:09 AM, Lovika Moudgil wrote: Hi Justin... Yes I agree my system is behaving absurdly . But I am wondering why !!I have done minimization without any error ..here is the result ... Steepest Descents converged to Fmax 1000 in 1004 steps Potential Energy = -9.6667906e+05 Maximum

Re: [gmx-users] il -simulation -reg

On 6/5/15 3:05 AM, Uma Devi wrote: Dear users, i am working in the ionic liquids simulation. i am having both anion and cation itp file. i have two query reagrding the simulation. 1. how did the two itp file be combined? Why would you need to? Typically, an .itp defines a single

Re: [gmx-users] .trr file

On 6/5/15 4:42 AM, Vy Phan wrote: Hi, Put the command line nstout, nstout (Output control-chapter 5-Gromacs manual) on your mdp file. Probably you mean nstxout, which is an .mdp keyword, not a command-line option. -Justin -- == Justin A.

Re: [gmx-users] gmx distance

On 6/5/15 7:07 AM, Ming Tang wrote: Dear gromacs experts, I am stretching a triple helix along z direction by fixing one end and pull the other. The helix length changes from 35nm to 50nm during the MD simulation. However, after using gmx distance -n index.ndx -f traj.trr -s topol.tpr

[gmx-users] gmx distance

Dear gromacs experts, I am stretching a triple helix along z direction by fixing one end and pull the other. The helix length changes from 35nm to 50nm during the MD simulation. However, after using gmx distance -n index.ndx -f traj.trr -s topol.tpr -select 'com of group start plus com of

Re: [gmx-users] GPU acceleration

Thanks for the info. I tried with GMX_EMULATE_GPU=1 preceding the mdrun line, crashed after 100 steps. Is that the expected behavior? On Fri, Jun 5, 2015 at 2:46 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Fri, Jun 5, 2015 at 10:39 PM, Alex nedoma...@gmail.com wrote: In that case, I am

Re: [gmx-users] GPU acceleration

On Fri, Jun 5, 2015 at 10:39 PM, Alex nedoma...@gmail.com wrote: In that case, I am a bit lost, as I was sure GMXRC needed modification. :)). Since I never ran anything on GPU and have an mdrun line that looks like mdrun -nt 4 -s tpr -c final structure gmx mdrun -ntomp 4 No need to do

Re: [gmx-users] GPU acceleration

Hi Szilárd, Well, yes, it is an old CPU, but I am actually quite content with the ns/day performance it churns out on all four cores. I'm looking at http://manual.gromacs.org/documentation/5.1-beta1/user-guide/environment-variables.html and it is my understanding that GMXRC needs to be changed to

Re: [gmx-users] GPU acceleration

Hi Alex, Why do you think GMXRC needs to be changed? You simply need to set those env. vars to trigger the GPU code-path - and you will likely have to freeze the system, otherwise it will probably not run more than a few steps without seeing an explosion. Based on this you'll know how fast you

[gmx-users] Error

I have run the following command on the Cluster server and I got the following error. Can anyone Please help me why I am facing this error. gmx mdrun -deffnm nvt_2 -v Reading file nvt_2.tpr, VERSION 5.0.4 (single precision) Changing nstlist from 10 to 25, rlist from 1.4 to 1.433 Will use 108

Re: [gmx-users] Error

the error message is self-explaining and provides the web link you should have followed before posting here (you should also have checked the mailing before posting, this is a recurring topic) On Fri, Jun 5, 2015 at 5:55 PM, chitrala kumaraswamynaidu cksna...@gmail.com wrote: I have run the

Re: [gmx-users] GPU acceleration

Hi Alex, That's a quite old CPU so it's hard to tell how fast is it, you'll have to try. There are ways to guesstimate how fast does your GPU have to be to keep up with your CPU cores (hint search for GMX_EMULATE_GPU / GMX_NO_NONBONDED on the list). In any case, unless your CPU is so slow that

Re: [gmx-users] GPU acceleration

In that case, I am a bit lost, as I was sure GMXRC needed modification. :)). Since I never ran anything on GPU and have an mdrun line that looks like mdrun -nt 4 -s tpr -c final structure what should be added to trigger the behavior you're suggesting? I understand that it will likely blow up the

[gmx-users] OPLS definition of Phenyl palmitate

Dear list, I ran into some problem to define the topology of phenyl palmitate. My main problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of the molecule without hydrogen (I hope it turns out to be readable in the email): O17

Re: [gmx-users] .trr file

hello, Yeah nst options worked perfectly.Thank you very much for the valuable comments. RegardsSwapnil On Friday, 5 June 2015 10:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/5/15 4:42 AM, Vy Phan wrote: Hi, Put the command line nstout, nstout (Output control-chapter