Re: [gmx-users] Implicit Solvent and Box Size

Dear Justin, Thank you for your suggestions! So what I have done is right. For implicit solvent, I just need turn on the options in .mdp file and no .itp file is needed to be included in the topology file. (I have tried but get errors). Thanks! Regards, Zhuo -- Gromacs Users mailing list *

Re: [gmx-users] Implicit Solvent and Box Size

On 10/7/19 11:12 AM, zhangzhu...@hotmail.com wrote: Dear Paul, Thanks for your advice. Since my system is acidic, I thought implicit solvent would get better approximation as I read from the GROMACS website. So there was no idea about my problem? Implicit solvent is used without PBC and

Re: [gmx-users] Implicit Solvent and Box Size

Dear Paul, Thanks for your advice. Since my system is acidic, I thought implicit solvent would get better approximation as I read from the GROMACS website. So there was no idea about my problem? Thanks! Zhuo -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Implicit Solvent and Box Size

Hi, I am doing the aggregations of small peptides in implicit solvents. However, it seems that there is no detailed tutorial on such subject and I just turned on the 'implicit solvent' option in the .mdp file. However, I found that the box was compressed during mdrun. It comes to me that the

Re: [gmx-users] Implicit Solvent and Box Size

Hello, the implicit solvent functionality has been deprecated a while ago in GROMACS and has been removed in the recent versions. Can the simulations also be run in explicit solvents (that are a better physical representation anyway)? Cheers Paul On 07/10/2019 16:50, 张 卓 wrote: Hi, I am

[gmx-users] Implicit Solvent and Box Size

Hi, I am doing the aggregations of small peptides in implicit solvents. However, it seems that there is no detailed tutorial on such subject and I just turned on the 'implicit solvent' option in the .mdp file. However, I found that the box was compressed during mdrun. It comes to me that the

Re: [gmx-users] Implicit Solvent with User Defined Potentials

Den 2019-05-08 kl. 16:21, skrev Akash Banerjee: Dear Gromacs Developer, I want to use the implicit solvent (gbsa algorithm) along with User-defined tabulated potentials. Apparently, the implicit solvent option is not compatible with the vdw-type=USer option. Can I please get some advice on

[gmx-users] Implicit Solvent with User Defined Potentials

Dear Gromacs Developer, I want to use the implicit solvent (gbsa algorithm) along with User-defined tabulated potentials. Apparently, the implicit solvent option is not compatible with the vdw-type=USer option. Can I please get some advice on this? Thank you for your help. Kind regards, Akash

Re: [gmx-users] Implicit solvent simulation

Hi, The implicit solvation implementation was broken with multiple threads for quite a few years, I'm afraid. So we have removed it for the upcoming 2019 release. I strongly recommend running it with only one thread (so use -ntmpi 1), or use the version in GROMACS 4.5.7 if you need the

[gmx-users] Implicit solvent simulation

Hello dear users! I'm trying to set up an implicit solvent simulation of a protein in gromacs, but I haven't found much about the details of how to do it. After generating topology: gmx pdb2gmx -f protein.pdb (I selected the amber99sb forcefield and none for water) I've done an energy

Re: [gmx-users] Implicit solvent

Hi, Implicit solvation works with multiple threads in GROMACS 4.5.x, but has been broken ever since (and will be removed in GROMACS 2019). So I suggest you use 4.5.7, or some other software (e.g. AMBER) Mark On Sun, Jun 24, 2018 at 4:00 AM Chhaya Singh wrote: > I am running implicit solvent

Re: [gmx-users] implicit solvent error

sorry i attached a wrong file. this is my inputs about the implcit solvent integrator = md dt = 0.005; ps ! nsteps = 2000 ; total 10 ns. nstlog = 5000 nstxout = 0 ;1000 nstvout = 0 ;1000

Re: [gmx-users] implicit solvent error

Your EM is unrelated to dynamics. I mean, it could, but we don't know anything about your simulated system. I am of course assuming that your MPI setup is optimal for gmx and you actually get to use those 16 threads, assuming those aren't an emulation of some sort. On 6/24/2018 1:33 AM,

Re: [gmx-users] implicit solvent error

Hi, I have attached the energy minimization mdp file. please look through it . cpp = /lib/cpp ; prepocessor of the current machine define = -DFLEXIBLE ; -DPOSRES,

Re: [gmx-users] implicit solvent error

This input has no information about implicit solvent and a simple google search immediately yields mdp examples using gbsa. As far as performance is concerned, we don't know the specs of your machine or the size of your system. With cutoff electrostatics and a cutoff of 5 nm, one can expect

[gmx-users] implicit solvent error

Hi, I am trying to simulate a protein in an implicit solvent in groamcs using amber ff99sb ildn . the mdpfile that I am using is I have shown below: integrator = md dt = 0.001 ;0.005; ps ! nsteps = 500 ; total 5 ns. nstlog =

[gmx-users] Implicit solvent

I am running implicit solvent in gromacs . I am getting very less speed 300 ps per day. Is there any way to increase the speed. -- 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

[gmx-users] Implicit solvent

: > I want to perform MD simulation using groamcs in implicit solvent. Can you > help me which force field is compatible with which solvent I can take? > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] Implicit solvent improvement in Gromacs 5.1.2

On Tue, Nov 8, 2016 at 6:46 PM, Mark Abraham wrote: > Hi, > > There's been no active work since 4.5 and no plans I've heard of. I hear > AMBER is pretty good at it on GPUs :-) > > Since Mark mentioned AMBER, just FYI for @Christian: AMBER have new and more accurate

Re: [gmx-users] Implicit solvent improvement in Gromacs 5.1.2

Hi, There's been no active work since 4.5 and no plans I've heard of. I hear AMBER is pretty good at it on GPUs :-) Mark On Wed, Nov 9, 2016 at 12:04 AM Christian Bope Domilongo < christianb...@aims.ac.za> wrote: > Dear all, > > There is any improvement of GB implicit solvent in Gromacs

[gmx-users] Implicit solvent improvement in Gromacs 5.1.2

Dear all, There is any improvement of GB implicit solvent in Gromacs package 5.1.2? Regards, -- 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

Re: [gmx-users] implicit solvent with periodic molecules

Hello again! My problem with implicit solvent is still unsolved. In gromacs manual and in gmx-users mail list was also mentioned that for implicit salvation all cut-offs should be switched to zeros. In that case PBC don't work. I've tried to perform simulation with implicit solvent and usual

Re: [gmx-users] implicit solvent with periodic molecules

On 11/3/15 3:36 AM, Анна Павловна Толстова wrote: Hello again! My problem with implicit solvent is still unsolved. In gromacs manual and in gmx-users mail list was also mentioned that for implicit salvation all cut-offs should be switched to zeros. In that case PBC don't work. I've tried to

[gmx-users] implicit solvent with periodic molecules

Hello, gmx_users. Is that possible to simulate a protein adsorption on graphite sheet with implicit solvent? It works good in vacuo and with explicit solvent with periodic-molecules = yes. But implicit solvent requires no PBC so that periodic molecules should be switched off too. Is there any

Re: [gmx-users] implicit solvent with periodic molecules

Yes. It is formally possible. I do not think that implicit solvation precludes PBC usage. On Thu, Oct 29, 2015 at 9:40 AM, Анна Павловна Толстова < tolst...@physics.msu.ru> wrote: > Hello, gmx_users. > > Is that possible to simulate a protein adsorption on graphite sheet with > implicit

[gmx-users] Implicit Solvent Gromacs 4.5.5, LINC errors in pulling simulations

Hi, I am running a pulling simulation with implicit solvent using Gromacs 4.5.5, single precision on 8 CPU, with OPLS-AA FFT. The system is equilibrated for 10 ns, with pbc=0 and infinite cut-off (.mdp file is posted). I do not get any LINC errors for the equilibration, however when I start

[gmx-users] Implicit Solvent Gromacs 4.5.5, LINC errors in pulling simulations

Hi, I am running a pulling simulation with implicit solvent using Gromacs 4.5.5, single precision on 8 CPU, with OPLS-AA FFT. The system is equilibrated for 10 ns, with pbc=0 and infinite cut-off ( .mdp file is posted). I do not get any LINC errors for the equilibration, however when I start

[gmx-users] implicit solvent concerns

Hi All, I am thinking of running an implicit solvent simulation using Gromacs (.mdp file pasted at the end of the email). However, I am a bit concerned about its accuracy as I get different results for the Polarisation term. More specifically, the first step of an energy minimisation gives

Re: [gmx-users] implicit solvent concerns

Hi, Stuff was probably broken here before 4.6. I would trust only single threaded in 4.6 and later, and only after comparing with 4.5. Mark On Mon, 11 May 2015 14:50 Albert Solernou a.soler...@leeds.ac.uk wrote: Hi All, I am thinking of running an implicit solvent simulation using Gromacs

Re: [gmx-users] implicit solvent concerns

Thanks for being so clear Mark. Best, Albert On 05/11/2015 03:18 PM, Mark Abraham wrote: Hi, Stuff was probably broken here before 4.6. I would trust only single threaded in 4.6 and later, and only after comparing with 4.5. Mark On Mon, 11 May 2015 14:50 Albert Solernou

[gmx-users] Implicit solvent in Gromacs 5.0.3

Hello all -- I recently installed a distribution of the new GROMACS 5, and I am finding myself in somewhat of a rut to perform implicit solvent simulations on the mpi-build. To put it simply, if I specify the cutoff-scheme as Verlet, GROMACS fails at grompp, because Implicit solvent is not (yet)

Re: [gmx-users] Implicit solvent in Gromacs 5.0.3

On 1/27/15 7:29 PM, Stephen Fried wrote: Hello all -- I recently installed a distribution of the new GROMACS 5, and I am finding myself in somewhat of a rut to perform implicit solvent simulations on the mpi-build. To put it simply, if I specify the cutoff-scheme as Verlet, GROMACS fails at

[gmx-users] Implicit solvent, Simulated annealing, Remove motion of center of mass

Hi all, The system I'm working with is Protein G (ID: 1PG) with a graphene surface using Implicit Solvent. I perform an energy minimization using steepest descent with 1000 steps and 0.001 ps time step. Then I use simulation annealing for 200ps to heat the system to 300K. After heating, the

Re: [gmx-users] Implicit solvent simulation of protein folding

UPDATE: I found these parameters to work: http://comments.gmane.org/gmane.science.biology.gromacs.user/52770 Now I have a follow up question. It seems that at 300K my unfolded protein chain quickly collapses into some random conformation and more or less stays that way without much