Re: [gmx-users] unstable system

Hi, The commands are as this: EM: minim.mdp : integrator    = steep        ; Algorithm (steep = steepest descent minimization) emtol        = 100.0      ; Stop minimization when the maximum force < 100.0 kJ/mol/nm emstep        = 0.01  ; Energy step size nsteps        = 5         

[gmx-users] query respect to perl distances.pl

Respected Sir Presently my work includes umbrella sampling for protein ligand interaction. The components of md_pull.mdp is title = Umbrella pulling simulation define = -DPOSRES_B ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nst

[gmx-users] line wrapping on the gmx-users list

The lack of line-wrapping makes it a pain to read. It happens to my emails that are posted on this list (and I have seen others), unless I put explicit line-breaks in my posts, which I often forget to do. Is there anything that can be done? IMHP, this should be automatically handled, and I oft

[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] Problem with Installing Gromacs 4.6.1 with GPU

I was trying to install gromacs 4.6.1 with CUDA and have a weird problem. My system is as the following new iMAC OS x 10.8.3 GPU : FTX 650 M 512 MB I also installed the open-mpi libraries into the /usr/local/lib folder before installation. I have got to say I'm by no means a UNIX expert. althou

Re: [gmx-users] g_dist

On 5/10/13 11:46 AM, mohammad agha wrote: Dear Justin, Thank you very much from your answer. May I ask you to help me more, Please? I work with UBUNTU, I don't know how should I do it! Apply Google. This is not a Gromacs issue and should be investigated and studied in the appropriate for

Re: [gmx-users] cudaStreamSynchronize failed

Hi, Such an issue typically indicates a GPU kernel crash. This can be caused by a large variety of factors from program bug to GPU hardware problem. To do a simple check for the former please run with the CUDA memory checker, e.g: /usr/local/cuda/bin/cuda-memcheck mdrun [...] Additionally, as you

[gmx-users] g_dist

Dear Justin, Thank you very much from your help. Best Regards Sara On 5/10/13 11:27 AM, mohammad agha wrote: > Dear GROMACS Specialists, > I have one problem with g_dist. When I use g_dist along with option -dist, > the output is printed on the terminal, but I want them into a file as > sepa

[gmx-users] g_dist

Dear Justin, Thank you very much from your answer. May I ask you to help me more, Please? I work with UBUNTU, I don't know how should I do it! Best Regards Sara On 5/10/13 11:27 AM, mohammad agha wrote: > Dear GROMACS Specialists, > I have one problem with g_dist. When I use g_dist along wi

Re: [gmx-users] g_dist

On 5/10/13 11:27 AM, mohammad agha wrote: Dear GROMACS Specialists, I have one problem with g_dist. When I use g_dist along with option -dist, the output is printed on the terminal, but I want them into a file as separately. May I ask you to help me, Please? Redirect the terminal output int

[gmx-users] g_dist

Dear GROMACS Specialists, I have one problem with g_dist. When I use g_dist along with option -dist, the output is printed on the terminal, but I want them into a file as separately. May I ask you to help me, Please? Thank you in advance Best Regards Sara -- gmx-users mailing listgmx-users@

[gmx-users] probability from COM of micelle

Hi, Thank you very much from your answer, but I think this is about numerical density (g(r)*(N/V)) or mass density (g(r)*(m/V))? I want to know about probability(nm^-1) with g_rdf, Please? Best Regards Sara - Forwarded Message - From: ABEL Stephane 175950 To: "gmx-users@gromacs.org"

Re: [gmx-users] Re: REMD average acceptance ratio

The replicas seem indeed to have exchange. Using a colour for the # replicas would help. I could not access to the first link. Note also that the increase of exchange ratio with the temperature suggest the distribution of the temperature is not optimal and may be with regular intervals? You

[gmx-users] Re: REMD average acceptance ratio

Dear gmx members, I have posted the same question previously , but I didn't get any reply. So, if anyone can help me out ... I performed a REMD simulation on a peptide 384 atoms (24 residues). In total 11 replicas were simulated for a period of 50ns each. The exchange was allwoed at every 1000 st

[gmx-users] g_cluster warning

hello everyone I am trying to cluster my data using g_cluster.I simulated the whole protein. I did the g_cluster analysis with only certain region of the protein which I specified using an index file.The program runs fine and gives 1 cluster.My concern is the warning it gives which states that :-

[gmx-users] probability from COM of micelle

Hi, Thank you very much from your answer, but I think this is about numerical density (g(r)*(N/V)) or mass density (g(r)*(m/V))? I want to know about probability(nm^-1) with g_rdf, Please? Best Regards Sara - Forwarded Message - From: ABEL Stephane 175950 To: "gmx-users@gromacs.org"

Re: [gmx-users] Problem importing PDB to Gromacs

On 5/10/13 5:16 AM, Jernej Zidar wrote: Hi, In CHARMM I generated a short peptide. The N-terminal is a regular -NH2 (patch NNEU) while the C-terminal is amidated (patch CT2). I would like to import the PDB to GROMACS using pdb2gmx by using the CHARMM27 forcefield later. I issue the foll

Re: [gmx-users] Difference between g_rms and g_rmsdist

On 5/10/13 4:24 AM, Nawel Mele wrote: Hi, I am trying to understand what is the difference between g_rms and g_rmsdist commands. I have looked at the manual and all I can find is that: *g_rms*: The root mean square deviation (RM SD) of certain atoms in a molecule with respect to a reference s

Re: [gmx-users] US and SMD

On 5/10/13 1:55 AM, Shima Arasteh wrote: Hi, In Umbrella Sampling method, among mdp settings, there is a section where the pull code settings are defined in: pull = umbrella: using a harmonic potential to pull As it is said that "with US the path of the permeating ion along thereaction coo

Re: [gmx-users] groups selection make_ndx -f npt.gro

On 5/10/13 12:35 AM, Arunima Shilpi wrote: Hello sir As in the tutorial for umbrella sampling command make_ndx -f npt.gro you have selected two different groups as Chain_A as 19 and Chain_B as 20 If we have protein-ligand interaction whether we should have single group of protein-ligand comp

[gmx-users] probability from COM of micelle

Hi, You indeed could use the g_rdf command like this (in the script) g_rdf_mpi -f "$pathXTC" -s "$pathTPR" -n bOG_Micelle_RDF.ndx -norm -com -b $timeBegin1 -e $timeEnd1 -o "$name1"_"$name2"_"$name3"_"$i"_original.xvg < RadDensFunc_"$i".txt Where in the RadDensFunc.txt file, i choose as the f

[gmx-users] Problem importing PDB to Gromacs

Hi, In CHARMM I generated a short peptide. The N-terminal is a regular -NH2 (patch NNEU) while the C-terminal is amidated (patch CT2). I would like to import the PDB to GROMACS using pdb2gmx by using the CHARMM27 forcefield later. I issue the following command: pdb2gmx -v -f irik-l.pdb -inte

[gmx-users] Difference between g_rms and g_rmsdist

Hi, I am trying to understand what is the difference between g_rms and g_rmsdist commands. I have looked at the manual and all I can find is that: *g_rms*: The root mean square deviation (RM SD) of certain atoms in a molecule with respect to a reference structure can be calculated with the progra

Re: [gmx-users] mdp-settings for charmm36 and lipid apl values

Hi, in addition to Chris' comments, I think one good way for getting APL of a lipid mixture is the one proposed by Edholm and Nagle : http://www.cell.com/biophysj/abstract/S0006-3495%2805%2972827-7. The idea is to run simulations at different concentrations of [A] and [B]. Ciao, Patrick Le 09/