[gmx-users] mdp file

Hi I want to creat mdp file for energy minimization (em.mdp). if I want to minimize my system (pr+dna), by steepest descent and conjugate gradient such as for example 100 steps by steepest descent and 100 steps by conjugate gradient, how I can creat mdp file? _

[gmx-users] mdp file

dear Mark thanks for your attention. is this mdp file true for energy minimization (100 steps by steepest descent and 100 steps by* conjugate gradient*)? define= -DFLEX_SPC constraints = none *integrator = steep nsteps = 100 integrator =

[gmx-users] mdp file

Hi all users, When I use the command "mdrun -tablep table.xvg " to run my model in gromacs, it always shows that: starting mdrun 'DNA in water' 1 steps, 20.0 ps. Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger than the 1-4 table size 1.000 nm These are ign

[gmx-users] .mdp file

Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp file. My question: If I wa

[gmx-users] mdp file

Hi gromacs users I want compare simulation of protein with simulation of protein-dna. should conditions (mdp file[T, P, dt, steps, ..] and box size) be same in two simulations? thanks alot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] .mdp file

Hey hi i want to do gromacs tutorial and for that i required the .mdp file for where i can get that file and what type of modification should i do in that file With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West Bengal State, India.-- gmx-users mailin

Re: [gmx-users] mdp file

leila karami wrote: Hi I want to creat mdp file for energy minimization (em.mdp). if I want to minimize my system (pr+dna), by steepest descent and conjugate gradient such as for example 100 steps by steepest descent and 100 steps by conjugate gradient, how I can creat mdp file? For exampl

Re: [gmx-users] mdp file

leila karami wrote: dear Mark thanks for your attention. is this mdp file true for energy minimization (100 steps by steepest descent and 100 steps by/ conjugate gradient/)? define= -DFLEX_SPC constraints = none *integrator = steep nsteps = 1

[gmx-users] mdp file help

Hi guys, I'm new to Gromacs and seeking some input on my .mdp file for the production run. I want to perform simulation to check protein stability over time and the after that the stable protein will be used for protein-protein docking/interactions. I'm using cubic box (with 1nm pbc) with water

[gmx-users] mdp file warnings

Hi, I'm setting my system but when I run grompp I get a warning and the program terminates.  It says the following:  You are using  pressure coupling with absolute position restraints, this will give artifacts. Use refcoord_scaling option. I want to try it but i don't know where to change thi

Re: [gmx-users] mdp file

He, Yang wrote: Hi all users, When I use the command "mdrun -tablep table.xvg " to run my model in gromacs, it always shows that: starting mdrun 'DNA in water' 1 steps, 20.0 ps. This is orders of magnitude too short to expect a large conformational change to happen. Think nanosecon

RE: [gmx-users] mdp file

further suggestions, Thank you . Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL PROTECTED] Sent: Thursday, November 06, 2008 3:52 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdp file He, Yang wrote: >

Re: [gmx-users] mdp file

He, Yang wrote: Hi Mark, This is what I got when I use the command gmxcheck: Checking file traj.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 34 Last frame 1 time0.100 Item#frames Timestep (ps) Step 20.1 Time

RE: [gmx-users] .mdp file

You have to modify the input .mdp and run grompp again. The mdout.mdp is for information only. Andreas > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Andrea Muntean > Sent: 10 November 2008 12:42 > To: Gromacs Users' List &

Re: [gmx-users] .mdp file

I thought so. Thank you very much! Cheers Andrea 2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED]>: > > > Andrea Muntean wrote: >> >> Hello there, >> >> I have a practical question regarding the mdp file, regardless the >> system to simulate. Before I would run a md simulation, usually we >> have t

Re: [gmx-users] .mdp file

Andrea Muntean wrote: Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp f

Re: [gmx-users] mdp file

On May 15, 2010, at 9:28, shahab shariati wrote: Hi gromacs users I want compare simulation of protein with simulation of protein-dna. should conditions (mdp file[T, P, dt, steps, ..] and box size) be same in two simulations? Besides the box size, which be reduced, all the rest sho

Re: [gmx-users] .mdp file

On 9/08/2011 5:26 PM, manoj damale wrote: Hey hi i want to do gromacs tutorial and for that i required the .mdp file for where i can get that file The tutorial will tell you how to get it or create it. and what type of modification should i do in that file Whatever the tutorial suggests

Re: [gmx-users] .mdp file

Dear Mark, Excellent suggestion, i'll also follow it to be a good gromacs user. Perhaps reading books, literature, searching on-line resources, go through tutorial or manual is always evergreen idea, but a bit hard work needed (To be an expert). Thanks a lot. Best Regards sharma On T

[gmx-users] mdp file problem

Hi GROMACS users, i am in the midst of simulating a protein in water. I have modified a residue in my pdb file at position 182, using amber and then acpype.py. But after running the energy minimization step,using em.mdp file generated from acpype , following error comes. Steepest D

[gmx-users] mdp file help

I am trying to simulate a single wall CNT in a box filled with water for about 500 ps and 300K just to start and I am having trouble with the mdp file, basicly what should and should not be in it. I just want it generic to start and tune it up later. Here is what I have done so far along with links

Re: [gmx-users] mdp file warnings

On 12/17/12 8:55 AM, Eduardo Oliveira wrote: Hi, I'm setting my system but when I run grompp I get a warning and the program terminates. It says the following: You are using pressure coupling with absolute position restraints, this will give artifacts. Use refcoord_scaling option. I wan

Re: [gmx-users] mdp file warnings

GROMACS users Enviadas: Segunda-feira, 17 de Dezembro de 2012 11:57 Assunto: Re: [gmx-users] mdp file warnings On 12/17/12 8:55 AM, Eduardo Oliveira wrote: > Hi, > > I'm setting my system but when I run grompp I get a warning and the program > terminates.  It says the follo

Re: [gmx-users] mdp file warnings

On 12/17/12 9:06 AM, Eduardo Oliveira wrote: OK, so if i got this right all I have to do is add another line in the mdp file with refcoord_scaling = com? I thought that i had to make a substitution in one of the existing terms. Right, it's a new term entirely (see the manual). All keywords

Re: [gmx-users] mdp file warnings

Ok, Thanks a lot! De: Justin Lemkul Para: Discussion list for GROMACS users Enviadas: Segunda-feira, 17 de Dezembro de 2012 12:08 Assunto: Re: [gmx-users] mdp file warnings On 12/17/12 9:06 AM, Eduardo Oliveira wrote: > OK, so if i got this right al

[gmx-users] .mdp file for polymer

hello sir, I made nstvout and nstfout parameters to zero and frequency to update position coordinates alone (nstxout) to 1000.But still am getting only one frame when viewed the trajectory in VMD.It is an NVT ensemble.How can i get more than one frame?I think the timestep and nsteps i have giv

[gmx-users] .mdp file for polymer

Hello sir, On giving gmxdump its giving me an error saying "segmentation fault.My box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and with columb type=PME. I read from mailing list that PME calculations requires large amount of memory space.Is this an issue with dime

Re: [gmx-users] mdp file problem

madhumita das wrote: Hi GROMACS users, i am in the midst of simulating a protein in water. I have modified a residue in my pdb file at position 182, using amber and then acpype.py. But after running the energy minimization step,using em.mdp file generated from acpype , foll

Re: [gmx-users] mdp file problem

Thanks Justin, I must inform you that my pdb file has a modified cysteine residue having a mercury atom attached to the sulphur atom next to the residue having the atom 2700. Is the murcury atom creating any problem? I want to also know can I use amber forcefield in GROMACS for pdb files of lipid?

Re: [gmx-users] mdp file problem

madhumita das wrote: Thanks Justin, I must inform you that my pdb file has a modified cysteine residue having a mercury atom attached to the sulphur atom next to the residue having the atom 2700. Is the murcury atom creating any problem? I want Probably. Parameterizing such a species pro

Re: [gmx-users] mdp file help

You can get a typical mdp file from some tutorials. By the way, I think the topology is wrong. Thanks. On 7/18/07, Christopher Stiles <[EMAIL PROTECTED]> wrote: I am trying to simulate a single wall CNT in a box filled with water for about 500 ps and 300K just to start and I am having trouble

Re: [gmx-users] mdp file help

Probably, you've broken your line endings transferring to/from a Windows machine. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search befo

Re: [gmx-users] .mdp file for polymer

varsha gautham wrote: hello sir, I made nstvout and nstfout parameters to zero and frequency to update position coordinates alone (nstxout) to 1000.But still am getting only one frame when viewed the trajectory in VMD. Just like some other trajectory formats, you do have to open a structu

Re: [gmx-users] .mdp file for polymer

varsha gautham wrote: Hello sir, On giving gmxdump its giving me an error saying "segmentation fault. 99.9% of the time there is more information available. Check your stdout, stderr and the .log file. My box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and w

RE: [gmx-users] .mdp file for polymer

-users] .mdp file for polymer Hello sir, On giving gmxdump its giving me an error saying "segmentation fault.My box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and with columb type=PME. I read from mailing list that PME calculations requires large amount of m

RE: [gmx-users] .mdp file for polymer

: gmx-users@gromacs.org Subject: [gmx-users] .mdp file for polymer Hello sir, On giving gmxdump its giving me an error saying "segmentation fault.My box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and with columb type=PME. I read from mailing list that PME ca

[gmx-users] mdp file for local pressure

Dear sir, I am calculating local pressure by gromacs-localp. My .mdp file is following integrator = sd ; stochastic dynamics -> Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps

[gmx-users] mdp file settings for PME

Dear experts, I posted this message before but I think you did not see it since I noticed messages after this have been replied. I have a hydrocarbon system with no charged particles. Today In one of the GROMACS tutorials I saw the following setting in em.mdp file: fourierspacing = 0.12 ;fou

[gmx-users] mdp file for monitoring pair groups

I have created an mdp file with 202 groups for monitoring in the energygrps string. Being 201 of these aminoacids which interact with the 202nd which is the ligand. The problem is that I found out that this does not work properly, and also does not work the way I thought it would work. Well, the de

RE: [gmx-users] mdp file for local pressure

The error message explicitly tells you what is wrong: "Expected 2 elements for wall_atomtype, found 0" And looking in your .mdp file ... ;WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall= 2 wall_type= 9-3 wall_r_linpo

RE: [gmx-users] mdp file for local pressure

Of anirban polley Sent: Monday, May 18, 2009 7:39 PM To: gmx-users@gromacs.org Subject: [gmx-users] mdp file for local pressure --- Program grompp_mpi, VERSION 4.0.2_localpressure Source code file: readir.c, line: 454 Fatal error: Expected 2

[gmx-users] mdp file to calculate local pressure

Dear Sir, I want to calculate local pressure of the membrane (pressure variation with z -axis). I am using gromacs-localp packages. As I see that all types of errors coming from saying specifically the option of WALL in .mdp file. Actually I did not understand clearly what to do in the

[gmx-users] mdp file to calculate local pressure

Dear Justin, I am using gromacs-localp of version 4.0.2. for the calculation of local pressure. But I could not understand what I should put in the mdp file. Because when I tried by the following below mdp file, it does not even create tpr file. I have tried by different options as for example

[gmx-users] mdp file to calculate local pressure

Dear Sir, I am looking for local pressure where I am using gromacs-4.0.2_localpressure.tarpackage. I have download it from ftp://ftp.gromacs.org/pub/tmp The error which it gives during

Re: [gmx-users] mdp file settings for PME

jojo J wrote: Dear experts, I posted this message before but I think you did not see it since I noticed messages after this have been replied. I have a hydrocarbon Messages do not receive replies in any sort of order. Probably no one has had any relevant comments yet, or they live in a t

Re: [gmx-users] mdp file for monitoring pair groups

what is not working exactly? This should give you as output all the pair interacts and you can select the ones you want ... ?! On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote: I have created an mdp file with 202 groups for monitoring in the energygrps string. Being 201 of these aminoacids whic

Re: [gmx-users] mdp file for monitoring pair groups

The problem is that the .tpr file tells me that the monitoring is being made between all pairs. I want only the pairs aminoacid1-ligand, aminoacid2-ligand etc and not aminoacid1-aminoacid2. This kind of monitoring, i.e., between all possible pairs, gives me .edr files that are 1Gb or more in size.

Re: [gmx-users] mdp file for monitoring pair groups

Ragnarok sdf wrote: The problem is that the .tpr file tells me that the monitoring is being made between all pairs. I want only the pairs aminoacid1-ligand, aminoacid2-ligand etc and not aminoacid1-aminoacid2. This kind of monitoring, i.e., between all possible pairs, gives me .edr files that a

Re: [gmx-users] mdp file to calculate local pressure

anirban polley wrote: Dear Sir, I want to calculate local pressure of the membrane (pressure variation with z -axis). I am using gromacs-localp packages. As I see that all types of errors coming from saying specifically the option of WALL in .mdp file. Actually I did not unders

Re: [gmx-users] mdp file to calculate local pressure

anirban polley wrote: Dear Justin, I am using gromacs-localp of version 4.0.2. for the calculation of local pressure. But I could not understand what I should put in the mdp file. Because when I tried by the following below mdp file, it does not even create tpr file. I have tried by dif

Re: [gmx-users] mdp file to calculate local pressure

anirban polley wrote: Dear Sir, I am looking for local pressure where I am using gromacs-4.0.2_localpressure.tar package. I have download it from ftp://ftp.gromacs.org/pub/tmp