RE: [gmx-users] g_current

> -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Nilesh Dhumal > Sent: Tuesday, July 09, 2013 5:06 AM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] g_current > > Thanks for reply. > > Still I have a qu

RE: [gmx-users] Calculating shear viscosity using none-equilibrium MD: Viscosity dependent on acceleration magnitude

Hi, I am not an expert in non-EQ MD, but a simulation time of 1ns for a collective property in a honey-like substance like an IL sounds very short. However, from my colleagues in the group of Prof. Müller-Plathe, who applied non-EQ MD to derive viscosities, I heard that this method is quite relia

RE: [gmx-users] Stimulation stopped at 2ns

> -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Nuno Azoia > Sent: Monday, July 08, 2013 11:21 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Stimulation stopped at 2ns > > On 8 July 2013 22:12, Just

Re: [gmx-users] Xe atom

thanks for the reply.. I am planning to place Xe in the protein binding site ( just like a metal atom). I made a topology file with xe charge and mass. I have two options to implement the simulation. 1. like protein-ligand simulation. 2. replacing a number of solvent (water) molecules with xe in th

[gmx-users] cuda problem

Dear: I've installed a gromacs-4.6.3 in a GPU cluster, and I obtained the following information for testing: NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, known to cause performance loss. Switching to the alternative polling GPU wait. If you encounter issu

Re: [gmx-users] cuda problem

PS: the error message is referring the to *driver* version, not the CUDA toolkit/runtime version. -- Szilárd On Tue, Jul 9, 2013 at 11:15 AM, Szilárd Páll wrote: > Tesla C1060 is not compatible - which should be shown in the log and > standard output. > > Cheers, > -- > Szilárd > > > On Tue, Jul

Re: [gmx-users] cuda problem

Tesla C1060 is not compatible - which should be shown in the log and standard output. Cheers, -- Szilárd On Tue, Jul 9, 2013 at 10:54 AM, Albert wrote: > Dear: > > I've installed a gromacs-4.6.3 in a GPU cluster, and I obtained the > following information for testing: > > NOTE: Using a GPU wit

Re: [gmx-users] cuda problem

On 07/09/2013 11:15 AM, Szilárd Páll wrote: Tesla C1060 is not compatible - which should be shown in the log and standard output. Cheers, -- Szilárd THX for kind comments. do you mean C1060 is not compatible with cuda-5.0 toolkit? or it is not compatable with Gromacs-4.6.3?I only obtained th

Re: [gmx-users] Xe atom

Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will obviously not sit in the binding site Dr. Vitaly V. Chaban On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil wrote: > thanks for the reply.. I am planning to place Xe in the protein binding > site ( just like a metal atom).

[gmx-users] g_cluster

Hi, I have a qustion how to use g_cluster to judge convergence of the simulation of peptide ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-cluster-tp5009690.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

Re: [gmx-users] cuda problem

On Tue, Jul 9, 2013 at 11:20 AM, Albert wrote: > On 07/09/2013 11:15 AM, Szilárd Páll wrote: >> >> Tesla C1060 is not compatible - which should be shown in the log and >> standard output. >> >> Cheers, >> -- >> Szilárd > > > THX for kind comments. > > do you mean C1060 is not compatible with cuda-

Re: [gmx-users] g_cluster

On 7/9/13 6:10 AM, maggin wrote: Hi, I have a qustion how to use g_cluster to judge convergence of the simulation of peptide ? Clustering can give you some insight into how homogeneous your structural ensemble is. That is one way to assess convergence. -Justin -- ==

Re: [gmx-users] Get some specific frames of traj

I tried the tpr file for -s, but doesn't make difference. g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.01 of (3.6, 3.6, 6.3)' -seltype res_com -selrpos res_com -os Would you please give me suggestions? I found some resemble commands in mailing list but didn't find the

Re: [gmx-users] Which/What is the adequate overlap using g_BAR

On 7/8/13 4:27 PM, mike.ne...@stud.uni-due.de wrote: Dear Gromacs People, I want to calculate free energy differences between two states A and B using g_BAR. For this I read many papers concerning the overlap between neighboring sample windows (Delta H) but I am still wondering about the foll

Re: [gmx-users] Get some specific frames of traj

On 7/9/13 7:14 AM, Shima Arasteh wrote: I tried the tpr file for -s, but doesn't make difference. g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.01 of (3.6, 3.6, 6.3)' -seltype res_com -selrpos res_com -os Would you please give me suggestions? I found some resemble com

[gmx-users] Re: g_cluster

hi, Justin I read the paper Daura(1999) and other papers: "Ensemble-based convergence analysis of biomolecular trajectories"(2006) "Helix propensities of short peptide: Molecular dynamics versus bioinformatics" (2003) "Assessing equilibration and convergence in biomolecular simulation" (2002) bu

[gmx-users] the principle of pulling

Dear, i am doing some simulation about pulling alkane into my micelle in umbrella sampling. i want to ask somethin about the output result in the pullf.xvg file. In the file, there are two lines data, one is time and the other is force. I want to know how the force come? or is there any formul

[gmx-users] the principle of pulling

Dear, i am doing some simulation about pulling alkane into my micelle in umbrella sampling. i want to ask somethin about the output result in the pullf.xvg file. In the file, there are two lines data, one is time and the other is force. I want to know how the force come? or is there any formula a

[gmx-users] Re: Re: Which/What is the adequate overlap using g_BAR

Dear Gromacs People, I want to calculate free energy differences between two states A and B using g_BAR. For this I read many papers concerning the overlap between neighboring sample windows (Delta H) but I am still wondering about the following issue: I know, that there has to be an adequa

[gmx-users] Squishing or Stretching Membranes

Hello everybody, I had a question about trjconv. After one of my simulations has ended I want to use the final structure file to run some other simulations. However, what I want to do is run an NVT run using the average box size of the earlier run. Since the final structure file will most likely n

[gmx-users] Multiple LINCS Warnings in NVT Equillibration

I am simulating one urea molecule in water and am struggling with it nvt.log *The .mdp for energy minimization is* ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to

Re: [gmx-users] Squishing or Stretching Membranes

On 09.07.2013 16:11, Neha wrote: I had a question about trjconv. After one of my simulations has ended I want to use the final structure file to run some other simulations. However, what I want to do is run an NVT run using the average box size of the earlier run. Since the final structure file w

RE: [gmx-users] Re: Re: Which/What is the adequate overlap using g_BAR

Hi Mike, Your confusion might stem from a very simple issue. To see the overlap of the forward and backward distributions, you have to plot N(+Delta H(lambda=x) | lambda=y) and N(-Delta H(lambda=y) | lambda=x). That is, you have to plot the histogram for the negative of the energy difference

Re: [gmx-users] Multiple LINCS Warnings in NVT Equillibration

Try using -DFLEXIBLE in your minimization prior to running NVT. MZ On Tue, Jul 9, 2013 at 10:22 AM, ashish24294 wrote: > I am simulating one urea molecule in water and am struggling with it > nvt.log > > > > > *The .mdp for energy minimi

[gmx-users] Issue with g_lie

Hi Everybody, I want to use g_lie for my protein-drug complex to get binding energy ..i read some information that we need take care some issues if we used PME electrostatics.. Indeed i have used PME in my simulation.. Can any body explain which parameters to be taken care while running g_LIE an

[gmx-users] Re: Problem with Amber99SB-ILDN ff

I am using gromacs 4.5.5, I didn't tell you yesterday. I have been tried a lot of things, but without any success. One of that I think has to work fine, is with the NGLU nomenclature, but when I use it, I obtain this There is a dangling bond at at least one of the terminal ends and the force fiel

[gmx-users] Problem with running REMD in Gromacs 4.6.3

Dear GMXers, With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4 cores with OpenMP. There is Torque installed on the cluster build of 12-cores nodes, so I used the following script: #!/bin/tcsh -f #PBS -S

[gmx-users] why DGbind=0 ?

Hello: I am using glie to evaluate my ligand binding affinity with command: g_lie_d -f md.edr -o lie.xvg -ligand LIG but I obtained the following results: Opened md.edr as single precision energy file Using the following energy terms: LJ: Coul: DGbind = 0.000 (0.000) @title "LIE free ene

[gmx-users] Umbrella sampling- force vs time plots

Hello all, I am trying to understand the force vs time plots using Gromacs' umbrella sampling method. I am trying to pull a short polymer chain from the interior of a micelle and see what the PMF looks like. I use the following parameters to run the pulling simulation for 500ps to pull the polymer

[gmx-users] Frozen covalent bound atoms

Hi all, I would imagine this has been covered before, yet I don't think I have unearthed the right search inquiry yet. I want to make a dihedral angle along the length of a helical protein using the vectors (A, B, C), (B, C, D), where B is a C-alpha on the helix backbone, and A , C and D are f

Re: [gmx-users] Multiple LINCS Warnings in NVT Equillibration

On 7/9/13 10:22 AM, ashish24294 wrote: I am simulating one urea molecule in water and am struggling with it nvt.log *The .mdp for energy minimization is* ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describ

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

On 7/9/13 11:23 AM, Melchor S. wrote: I am using gromacs 4.5.5, I didn't tell you yesterday. I have been tried a lot of things, but without any success. One of that I think has to work fine, is with the NGLU nomenclature, but when I use it, I obtain this There is a dangling bond at at least o

Re: [gmx-users] the principle of pulling

On 7/9/13 8:09 AM, wanghua wrote: Dear, i am doing some simulation about pulling alkane into my micelle in umbrella sampling. i want to ask somethin about the output result in the pullf.xvg file. In the file, there are two lines data, one is time and the other is force. I want to know how the

Re: [gmx-users] Umbrella sampling- force vs time plots

On 7/9/13 12:56 PM, rookie417 wrote: Hello all, I am trying to understand the force vs time plots using Gromacs' umbrella sampling method. I am trying to pull a short polymer chain from the interior of a micelle and see what the PMF looks like. I use the following parameters to run the pulling

Aw: [gmx-users] Umbrella sampling- force vs time plots

  From running a bunch of these your pullf.xvg should look like a curve and taper off at the end (go down) or you didnt reach the maximum...with the force I had to play around and started with published work for similar proteins, but had to increase the force from 1000 (published) to 2000, so a la

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Sorry for the misunderstanding. I should had explained it better. I know that is a zwitterionic residue, I have run several simulations with the same PDB and with other forcefields. ACPYPE does not work, I tried it yesterday, but I have to check it. Antechamber I don't know, I have to try it. Als

[gmx-users] Re: gInstallation Problems with Gromacs4.6

Dear all, I call cmake the following way and get the error bellow: CC=mpicc CXX=mpicxx CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \ /lustre/utility/bin/cmake \ -DCMAKE_CXX_COMPILER=/xxx/xxx/intel/impi/4.1.1.036/intel64/bin/mpicxx \ -DCMAKE_C_

[gmx-users] How to apply trjconv -nojump to a part of a system

Hi All, For the convenience of visualization, I need to remove the jump of one component (say a protein) of the system at the boundary. I don't need to, or say I need not to remove the jump of the other components (say a lipid bilayer), since otherwise the system will look falling apart. I noticed

Re: Aw: [gmx-users] Umbrella sampling- force vs time plots

Thanks Justin and Stephan, One more question, while pulling from the interior of a multiple monomer micelle structure, I used higher force constants (5000 kJ/mol/nm^2) for position restraints on the reference group to keep the system intact. I am assuming that I have to use different pull_k1 for