Re: [gmx-users] How to write pull code in umbrella sampling

Thank you, Justin. My goal is to investigate the conformation transition of a 30aa loop between an unstructured loop and an alpha-helix. I found a transition pathway on free energy landscape and selected a number of frames along the pathway for umbrella sampling. So, should I define C-alpha

[gmx-users] Regarding gmx sorient

Hello, I have done md simulation of amino acid in solvent mixture, How can i calculate the gmx sorient..?? I am not able to understand anything in the link http://manual.gromacs.org/programs/gmx-sorient.html Is it like for calculating the RDF,(in which we have to first index the files and thn in

[gmx-users] failed to restart the REMD

Hi, I have run REMD for 80ns. But I can't restart the REMD. The errors are as following: Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(1339)...: MPI_Allreduce(sbuf=0x7fff4ac3fa90, rbuf=0x29af530, count=4, MPI_FLOAT, MPI_SUM, comm=0x8400) fai led

[gmx-users] How to write pull code in umbrella sampling

Dear Colleagues, I am trying to do an umbrella sampling using a series of conformations extracted from several unbiased MD trajectories. But I am not sure about the pull code in .mdp file. Below is the pull code from the tutorial of Dr. Justin Lemkul : define = -DPOSRES_B ; (Why ??) ;

Re: [gmx-users] Extending simulation

Thank you On Fri, 7 Apr 2017 at 5:33 PM, Justin Lemkul wrote: > > > On 4/7/17 5:07 AM, João Henriques wrote: > > Dear Rahul, > > > > I've never worked with gmx-2016, but the error message is extremely > clear. > > Therefore I will skip the explanation and just give you the

Re: [gmx-users] Md simulation by Gromacs

Dear Maria, Let’s keep this to the user list. I am first of all not a private tutor. Secondly, the answers you get (below) might be relevant for others. > On 6 Apr 2017, at 16:04, maria khan wrote: > > Good evening Dear sir Erik Marklund.. > > I am very Thankful

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] Extending simulation

On 4/7/17 5:07 AM, João Henriques wrote: Dear Rahul, I've never worked with gmx-2016, but the error message is extremely clear. Therefore I will skip the explanation and just give you the solution. Rename the old tpr as md_old.tpr (or something or the sort) and the new extended one as md.tpr.

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] determining restraints for pulling

On 4/7/17 1:43 AM, abhisek Mondal wrote: Is it possible to pull (distance pull) along negative of Z axis (for example, I'm saying Z) ? Do I need to mention -Z in pull code or the program improvises if I say Z axis distance pull in .mdp ? Yes, you can define a pull vector in the negative Z

Re: [gmx-users] Position restraint on DPPC lipid bilayer

On 4/7/17 1:20 AM, Sithara Perera wrote: Hi!, I' making a 512 DPPC bi-layer out of 128 bilayer available in http://www.cgmartini.nl. The force field used is martini. But once the energy minimization is done, the bi-layer crashes and accumulates to globules. So I made an position.itp

[gmx-users] GTX Titan XP performance for gromacs

Dear all, is anybody planing test GTX Titan XP, the consumer version of Quadro P6000 for gromacs. How do you expecting the performance with respect to GTX 1080 TI. Thanks in advance. Regards Dr. Santosh Kumar Postdoctoral Researcher Department of Chemistry and Biochemistry University of

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] Extending simulation

I forgot a small detail, you need to include "-deffnm md" to your mdrun command, as the error message clearly states. /J On Fri, Apr 7, 2017 at 11:07 AM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Dear Rahul, > > I've never worked with gmx-2016, but the error message is extremely

Re: [gmx-users] Extending simulation

Dear Rahul, I've never worked with gmx-2016, but the error message is extremely clear. Therefore I will skip the explanation and just give you the solution. Rename the old tpr as md_old.tpr (or something or the sort) and the new extended one as md.tpr. Then it shouldn't complain because all run

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