[gmx-users] Fwd: query

Hello, I want to calculate the energy of the two groups. I have defined those groups in mdp file. I want to run it for 5 ns. So, I set the nsteps and all parameters according to my need. Now I am using the rerun command for calculating the energy. But it is only giving the energies till 100 ps

[gmx-users] Fwd: Query regarding Preferential Interaction Coefficient Calculation

Dear all, I want to calculate the number of water and osmolyte molecule at particular distance from surface of protein in order to calculate preferential interaction coefficient. I had calculated it using gmx select command. Is it right to calculate using this command. Please help me in this

Re: [gmx-users] gromacs Query

thank you sir I have applied nstxout, nstvout, nstfout as zero and it is now working Thankyou On Fri, Apr 7, 2017 at 6:04 PM, Mark Abraham wrote: > Hi, > > On Fri, 7 Apr 2017 11:18 Aman Deep wrote: > > > sir, I didn't understand what is E

Re: [gmx-users] gromacs Query

Hi, On Fri, 7 Apr 2017 11:18 Aman Deep wrote: > sir, I didn't understand what is E here ??? > As Justin suggested, that was a typo for "maybe". and after removing nstxout still, it is not helping.. > I did not suggest doing that. I did ask what your GROMACS

Re: [gmx-users] gromacs Query

On 4/7/17 6:17 AM, Aman Deep wrote: sir, I didn't understand what is E here ??? I think Mark made a typo in writing the word "maybe" here. The point he was making is that you're trying to specify nstxtcout and nstxout-compressed, which is a mixture of syntax from different GROMACS

Re: [gmx-users] gromacs Query

sir, I didn't understand what is E here ??? and after removing nstxout still, it is not helping.. On Fri, Apr 7, 2017 at 1:25 PM, Mark Abraham wrote: > Hi, > > Which version of GROMACS is this? The only problem I can see is that you > are using both nstxtcout and

Re: [gmx-users] gromacs Query

Hi, Which version of GROMACS is this? The only problem I can see is that you are using both nstxtcout and its successor (don't), and may E that is confusing the parser. Mark On Fri, 7 Apr 2017 07:41 Aman Deep wrote: > sir, i am using this output control but still, it

Re: [gmx-users] gromacs Query

sir, i am using this output control but still, it is generating same space data ; Run parameters integrator = md; leap-frog integrator nsteps = 2500 ; 2 * 50 = 5 ps (50 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0

Re: [gmx-users] gromacs Query

Hi, If you ask for .trr output, you get it. Stop using non-zero nst*out mdp settings that you don't want. Mark On Mon, Apr 3, 2017 at 11:31 AM Aman Deep wrote: > sir, > > I have tried *nstxctout *but it still making trr file ... is there any > option to make only

Re: [gmx-users] gromacs Query

sir, I have tried *nstxctout *but it still making trr file ... is there any option to make only xtc file ??? On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham wrote: > Hi, > > See > http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_ > Volume > >

Re: [gmx-users] gromacs Query

Hi, See http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark On Mon, Apr 3, 2017 at 9:27 AM Aman Deep wrote: > sir is there any way to create only XTC file from mdrun only. the server on > which I am working is not providing enough

[gmx-users] gromacs Query

sir is there any way to create only XTC file from mdrun only. the server on which I am working is not providing enough space and my trr file is too much large. thank you -- Aman Deep MSc Bioinformatics Jamia Millia Islamia New Delhi - 110025 -- Gromacs Users mailing list * Please search the

[gmx-users] Unanswered Query regarding hydrogen bond lifetime and energy

> Dear All, > Let me repeat my earlier query. > I'm trying to calculate the hydrogen bond lifetime in my system (water-ethanol) using command g_hbond -f traj.trr -s md.tpr -n index.ndx -ac -life hblife.xvg. It is peculiar to note that when I select index groups as OW and HW (for water), it finds

[gmx-users] A query about nsteps

Dear gromcas users, I carried out a continuation of previous md run for nsteps of 500 and dt of 0.002 using the following commands, gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi md1.cpt -deffnm md2 The mdp file following run

Re: [gmx-users] A query about nsteps

On 8/20/15 7:49 AM, anu chandra wrote: Dear gromcas users, I carried out a continuation of previous md run for nsteps of 500 and dt of 0.002 using the following commands, gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n index.ndx -p topol.top gmx_mpi mdrun -cpi

[gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations

i want to simulate a system having membrane and proteins with pbc=no to allow surface effects. I use the following settings in my production mdp file : Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 ms dt =

Re: [gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations

Why is this urgent? Have you tried the suggestions given by the program? Cheers, Tsjerk On Wed, Jun 3, 2015 at 12:08 PM, Antara mazumdar antara.mazum...@igib.in wrote: i want to simulate a system having membrane and proteins with pbc=no to allow surface effects. I use the following settings

Re: [gmx-users] A query

Thank you all for the reply. On Mon, Apr 13, 2015 at 6:39 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Yes, there are a few programs in computational chemistry that give such quotes randomly; GAUSSIAN comes to mind. There's an environment variable described in one of the manual

[gmx-users] A query

Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers)* Such messages pop up after running the gromacs commands on terminal. Do these messages have any meaning ? Have they anything to do with the programs we are running? -- *Let us all join hands to save

Re: [gmx-users] A query

Hi Priya, Yes, this particular message means that you should also get to know yourself, because it is key to understand others, which is the most important step to not being lonely. This one may not be directly related to the program, but in terms of science, it sort of suggests that you should

Re: [gmx-users] A query

Nope! They are just for our amusement. Maybe only one has to do it: Check your input! David van der Spoel Cheers! Marcelo Depólo Em 13/04/2015 07:05, Priya Das priyadas...@gmail.com escreveu: Dear All, *gcq#6: It's So Lonely When You Don't Even Know Yourself (Red Hot Chili Peppers)* Such

Re: [gmx-users] A query

Hi, Yes, there are a few programs in computational chemistry that give such quotes randomly; GAUSSIAN comes to mind. There's an environment variable described in one of the manual appendices that will disable them, if you prefer. Mark On 13/04/2015 12:25 pm, Tsjerk Wassenaar tsje...@gmail.com

[gmx-users] FW: Query regarding performance varies hugely in two similar systems

Dear Gromacs users, Sorry if you are receiving this email twice! I am trying to study a self-assembly process of a polymer with three different composition ratio using Gromacs in CPU cluster (Intel(R) Xeon(R)). As the ratio of the polymer constituents are different, the number of atoms differs