Re: [gmx-users] surprising: what's the reason?

Hi Chetan, nstenergy = 1 requires nstcalcenergy = 1, which requires nstlist = 1. You might want to try setting only the latter, and check nstpcoupl. Hope it helps , Tsjerk On Mar 16, 2014 7:17 AM, Chetan Mahajan chetanv...@gmail.com wrote: Hi Mark, Tsjerk and others interested, I changed

Re: [gmx-users] Rigid water model

On Mar 14, 2014 11:06 PM, Michelle Aranha mara...@utk.edu wrote: Hi! I tried to reproduce results for rigid water with 895 molecules~1000 kg/m3 density, 10 ns NPT simulation (298 K 1 bar)with Parinello Rahman Barostat and Berendsen thermostat. Using a thermostat that produces the wrong

Re: [gmx-users] Rigid water model

Setting the compressibility in gromacs actually is just as way adjust the stiffness of the barostat. Berendsen thermostat guarantees a Cp that is too low. Try v-rescale or nose-Hoover. See http://pubs.acs.org/doi/abs/10.1021/ct300688p For more info. Sent from my iPhone On Mar 16, 2014, at

Re: [gmx-users] genion

On 3/16/14, 9:49 AM, Andrew Bostick wrote: Dear Kalyan Thanks for your reply I want to use Zn2+ ions with my protein. There is Zn2+ ions in atomtypes.atp file of opls force field. But there is not Zn2+ ions in ions.itp file of of opls force field. Based on your answer, now, I can not use

Re: [gmx-users] Interaction energy graph

On 3/16/14, 12:49 AM, kannan wrote: Dear Justin, sorry sir i forget to attahc the files, it is here attached. Thank you very much for your reply.. I answer the above question, 1. I am doing the protein-ligand interaction(electrostati+vanderWaals). I took the 140 amino acid as a sequence which

Re: [gmx-users] excuse me, I want to ask you some question about bond energy

On 2014-03-16 13:56, scuwangyu...@126.com wrote: Hi, David: I am very sorry to bother you! I would like to ask you some questions because you are an expert and ever answered the message about bonds energies calculation in Gromacs forum. yakovenko have introduced the methods in detail using

[gmx-users] enthalpy of ion + protein interaction

Dear gromacs users I want to obtain enthalpy of Cu2+ + my protein interaction. How to calculate that? Is g_energy appropriate for my case? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] binding delta G, H and S for ion-protein

Dear groamcs users I want to calculate binding delta G. I know g_lie tool is used to calculate delta G for protein-ligand or enzyme-drug binding. Can I use g_lie tool o calculate delta G for binding some ions to one protein molecule? Generally, which toolS of gromacs are appropriate for

Re: [gmx-users] Rigid water model

V-rescale as thermostat does give approximately the correct value for Cp. Thanks!! -- View this message in context: http://gromacs.5086.x6.nabble.com/Rigid-water-model-tp5015158p5015202.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list *

Re: [gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel

Hi Szilárd , To 7) this step avoids the error reported at the following link by using Marks' workaround: http://gromacs.5086.x6.nabble.com/mdrun-I-O-or-system-error-No-such-file-or-directory-td5013900.html#a5013901 As far as finding the FFTW library is concerned, I agree that the paths

Re: [gmx-users] enthalpy of ion + protein interaction

Hi Andrew, For such ions you'll need QM methods to properly describe the interactions with a protein. Cheers, Tsjerk On Mar 16, 2014 4:22 PM, Andrew Bostick andrew.bosti...@gmail.com wrote: Dear gromacs users I want to obtain enthalpy of Cu2+ + my protein interaction. How to calculate