Re: [gmx-users] COM-COM distance: PBC problem

Hi Arnost, When you fit with rotation the coordinates and the box are not on par anymore. Anything you do after that tries using PBC will fail. I guess that Plumed is trying to use the box to get the COM-COM distance. The only (practical) solution: don't fit. Cheers, Tsjerk On Aug 17, 2016 00:2

Re: [gmx-users] CPU running doesn't match command line

Hello: Here is the information that you asked for. gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 0 -pin on -

Re: [gmx-users] HID error in amber14sb.ff

Hi, I had this problem and wrote to Viet Man who uploaded the force field. I am quoting his answer: I have found the error come from HIP residues, diheral angle CB-CG-CD2-ND1 (= CT-CC-CW-NA). It causes by missing the improper dihedral angle information. To solve it, you may open file ffbonded.itp

Re: [gmx-users] TPI and chemical potential

Thanks again In my hands at least, -pbc mol -ur compact seems to be necessary, as without it I get a lot of instead of actual numbers. I tried to find a reference for the chemical potential of TIP3P, but haven't succeeded yet. Related to gromacs, I find one thread in the archives that claims tha

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 63

Hi Tsjerk, thank you so much for your advice. I totally agree with you - up to the fitting step, everything is OK. Yet, fitting to chain-A is clearly inevitable for me (at least the rotational fit) as I want to study the movement (sampling) of Chain-B’s COM (in x,y,z coordinate space) with resp

[gmx-users] g_select water

Dear all, I have a cylinder protein (like single-wall carbon nanotube) solvated in water. I wonder how I can use g_select to select all the water inside the protein. Best, Yao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_L

[gmx-users] g_select water

- Dear all, I have a cylinder protein (like single-wall carbon nanotube) solvated in water. I wonder how I can use g_select to select all the water inside the protein. Best, Yao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

[gmx-users] NEMD of membrane protein

Dear Sir, I'm trying to mimic osmotic pressure condition on a membrane protein in gromacs by applying constant force (through constant accelearation) on group of water molecules in z-direction in the simulation box through Non-equilibrium MD option in mdp file. I have following question

Re: [gmx-users] TPI and chemical potential

I think the Widom particle insertion method can also apply to NPT as long as the volume fluctuations are taken into account (see equation 2.69b in Allen and Tildesley's Computer Simulation of Liquids ). From what I recall from the code, I think they are. Do not forget the result is the excess chem

[gmx-users] g_select water

- Dear all, I have a cylinder protein (like single-wall carbon nanotube) solvated in water. I wonder how I can use g_select to select all the water inside the protein. Best, Yao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

[gmx-users] GPU HW questions

Hello, I have 2 processor Xeon E5-2660 node and I want to add the GPU. I'm thinking about Radeon Fury (without X) which I can get bellow 350 eur, or 2 pcs. of RX 470. My systems have usually between 100 000 and 200 000 atoms - I suppose it can influence the CPU-GPU ratio. Or do you think somethi

Re: [gmx-users] GPU HW questions

Processor speed and cores matters and I believe you can try GeForce Cards cards like GTX 1070 which is faster and cheap. http://arxiv.org/abs/1507.00898 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Ca

Re: [gmx-users] HID error in amber14sb.ff

Hi, Thanks a lot for helping. You are right about the atom types of each atom within this error, which are CB-CG-CD2-ND1. And I followed your logic to add one line to file ffbonded.itp. Do I need to do anything else to let gromacs load the file? because adding this line won't solve the error.

Re: [gmx-users] HID error in amber14sb.ff

Sorry about the continuous email. I think I solved this issue. For HID and HIP, they used different atom types for CD2. CV for HID and CW for HIP. Thanks for helping. --Hongbin On Wed, Aug 17, 2016 at 10:53 AM, Hongbin Wan wrote: > Hi, > > Thanks a lot for helping. > > You are right about th

[gmx-users] Diffusion coefficient water

Dear Gromacs users, I was trying to reproduce the published values for the diffusion coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my simulations and I am failing to do so. More worryingly I get different results for different identical runs. I am using a 2n

Re: [gmx-users] Diffusion coefficient water

I don't think we can reproduce the exact results in MD .The overall behaviour of the system will be same .so it's obvious -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.groma

Re: [gmx-users] Diffusion coefficient water

On 8/17/16 11:28 AM, Diez Fernandez, Amanda wrote: Dear Gromacs users, I was trying to reproduce the published values for the diffusion coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in some of my simulations and I am failing to do so. More worryingly I get differen

[gmx-users] is there martini CG parameters for K+ ion?

Dear gmxers, I am not sure if I'd better post my question here, but the martini forum http://www.cgmartini.nl/index.php/forum does not allow me register and post my question there. I am trying to simulate some KCl solution, but only find martini CG Na+ parameters at http://cgmartini.nl/images/para

Re: [gmx-users] Diffusion coefficient water

I think you could try following things to see if you could get 'better' results 1. use time step of 0.2 or even 0.1 fs 2. try different tau-t and tau-p, e.g. use larger tau-t 3. try different p-coupling methods 2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk>: > D

[gmx-users] Fwd: is there martini CG parameters for K+ ion?

Dear gmxers, I am not sure if I'd better post my question here, but the martini forum http://www.cgmartini.nl/index.php/forum does not allow me register and post my question there. I am trying to simulate some KCl solution, but only find martini CG Na+ parameters at http://cgmartini.nl/images/para

Re: [gmx-users] Diffusion coefficient water

4. you could even try NVT ensemble 2016-08-18 2:25 GMT+08:00 li he : > I think you could try following things to see if you could get 'better' > results > 1. use time step of 0.2 or even 0.1 fs > 2. try different tau-t and tau-p, e.g. use larger tau-t > 3. try different p-coupling methods > > 201

[gmx-users] Gromacs 2016 building issue

Hello, I just tried building Gromacs2016. The build went fine until it reached the linking stage: linking CXX executable ../../bin/template /opt/pkg/2015Q2/lib/libxml2.so.2: undefined reference to `gzopen64' collect2: error: ld returned 1 exit statu

Re: [gmx-users] CPU running doesn't match command line

anybody has more suggestions? thx a lot On 08/17/2016 09:07 AM, Albert wrote: Hello: Here is the information that you asked for. gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 0 -pin on