[gmx-users] LINC warning after long time simulations

Hi All: I pasted this once several days ago but no one replied. I know there are a lot of questions in the forum regarding LINC warning, but my problem seems quite strange. So I write here again. My simulation system contains lipids and proteins, I am using gromos53a6 for the proteins and

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

Dear Sebastian, I have some trouble reading your top file in my web browser but I think your transformations are IPX->Na+, IMX->Cl-. So you would have to reverse the columns for the first atom. As your two dummy types appear to be identical you can define just one. Cheers, Hannes.

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

Dear Hannes, Thank you very much for your answer. > Practical question: why would you want to do that? > Your two molecules will drift apart unless parts of the molecules are > linked together in a "single" topology fashion or or you introduce > other restraints/constraints. I am doing some

Re: [gmx-users] Example of H REMD

Was this not useful? > Most of this should still be applicable for 5.0.4. > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy On Mon, Nov 30, 2015 at 8:51 AM, Sanja Zivanovic wrote: > Dear users, > > Could you please send

[gmx-users] Example of H REMD

Dear users, Could you please send me some example of inputs for Hamiltonian Replica exchange? It would be great if you can write me command line and attach mdp file. I would like to make H REMD for following ligand. Thanks in advance a lot Best Regards, Sanja -- *Sanja Zivanovic* PhD Student

Re: [gmx-users] tutorial umbrella sampling

Thanks, that did the trick! Now everything works fine. Am 29.11.2015 um 12:00 schrieb gromacs.org_gmx-users-requ...@maillist.sys.kth.se: On 11/27/15 5:36 PM, Matthias Kiesel wrote: Hi All, I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have a problem with

Re: [gmx-users] Fwd: removing some atoms

I am not sure how familiar with programming, but my usual approach is to simply insert the molecules and then write a program that removes the solvent residues whose atoms are too close to the protein. Another approach would be to use gmx solvate to solvate your protein as usual and then write a

Re: [gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

Hi Justin, Thanks for the reply. I have few more doubts. I had mentioned CHARMM27 just for consistency with Gromacs naming. In the website it mentions that those settings are for CHARMM36 and I read at lot of places that this force field is good mainly for membrane proteins, so is it ok for

Re: [gmx-users] LINC warning after long time simulations

Hi, When you see the LINCs warning it does not mean that your simulation is going wrong if there is no error or segmentation fault. In most case, the warning is due to bad energy minimization step or if ther is blowing up it can be due to  bad topology which by modifying them it can be solved.

[gmx-users] extracting coordinates from traj.xtc

Dear all, I have some problems extracting data from traj.xtc. The command " g_traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again couldn't get any results. Note that I have nstxtcout = 1 and xtc_grps = water in my .mdp file. Any help is appreciated. Thank you! --

[gmx-users] topology of ligand contains boron

Dear, im currently running MD simulation of protein-ligand complex. but the ligand that im running contain boron. i failed to obtain the ligand topology from PRODRG, thus my analysis cant progress since then. would like to ask for opinion how can i solve this situation.? thanks. Best regards,

Re: [gmx-users] topology of ligand contains boron

Hi all, Can someone please answer my question, about how to find forces on the atoms of the "frozen" molecule/group. Thanks Subn Sent from my HTC - Reply message - From: "Low Chen Fei" To: Subject: [gmx-users]

[gmx-users] Fwd: removing some atoms

Hi all, I sent this few days ago and I am still struggling with this, any help,hints is highly appreciated. -- Forwarded message -- From: James Lord Date: Thu, Nov 26, 2015 at 11:18 PM Subject: removing some atoms To: "gmx-us...@gromacs.org"

Re: [gmx-users] Fwd: removing some atoms

There are some automated tools for membrane insertion that you can probably modify for you use, but I would probably just try a manual insertion followed by a long equilibration. For the membrane insertion you have this tutorial which uses InflateGRO:

Re: [gmx-users] topology of ligand contains boron

On 11/30/15 7:09 AM, subho_1...@yahoo.com wrote: Hi all, Can someone please answer my question, about how to find forces on the atoms of the "frozen" molecule/group. Please don't hijack unrelated threads. Advice via this list is contributed for free by people who have available time. I

Re: [gmx-users] topology of ligand contains boron

On 11/30/15 3:19 AM, Low Chen Fei wrote: Dear, im currently running MD simulation of protein-ligand complex. but the ligand that im running contain boron. i failed to obtain the ligand topology from PRODRG, thus my analysis cant progress since then. would like to ask for opinion how can i

Re: [gmx-users] Errors pdb2gmx

On 11/30/15 7:53 AM, Stefania Evoli wrote: Hi everybody, I’m simulating for the first time the riboswitch in presence of metals, usually I work only with proteins. I modified the pdb file to have the 5’ and 3’ terminals but when I try to use pdb2gmx_mpi_d (Gromacs 5.0.5) to generate gro and

Re: [gmx-users] topology of ligand contains boron

It is not polite to ask again after just a few hours, since we are here doing this for free (you cannot push people into answering your questions, after all they are yours, not ours). If you have chosen to work with an exotic molecule with missing parameters of any kind, it is you job to fill the

Re: [gmx-users] seeking a little help

On 11/30/15 12:04 AM, Subho Chakraborty wrote: Hi All, I am a new student of molecular dynamics. I have started using GROMACS since one month. I have a small question to pose to anyone who is happy to help me. I have a small box of 8192 molecules each with 3 atoms. I have frozen the last

[gmx-users] Errors pdb2gmx

Hi everybody, I’m simulating for the first time the riboswitch in presence of metals, usually I work only with proteins. I modified the pdb file to have the 5’ and 3’ terminals but when I try to use pdb2gmx_mpi_d (Gromacs 5.0.5) to generate gro and top file with the ff amber99sb-ildn I get the