Re: [gmx-users] Pressure control with constraints incompatible with expanded ensemble

Hi, Jacob- Unfortunately, that is correct. We had though we'd have functionality that could support this combination in 2018 (a Monte Carlo barostat and/or expanded ensemble in alchemical space working with leapfrog), but those did not make it in. The support for MTTK with constraints was

Re: [gmx-users] Fwd: Adding new atom types

I'm not sure off the top of my head. The manual says: "Pair parameters that are not present in the [ pairtypes ] section are only generated when gen-pairs is set to “yes” in the [ defaults ] directive of forcefield.itp" so it sounds like the parameters in the [ pairtypes ] section should be

[gmx-users] External sinusoidal force

Hi all, I asked this before and I think I remember the answer, so this is just to make sure, before we move to another software package. 1. We need a sinusoidal force of given direction, amplitude, and frequency applied to a selected group of atoms. Mimicking it with giving those atoms charge

[gmx-users] minimization is not converging (Bratin Kumar Das)

>> getting failed for my system Not clear to me. What are the errors? Did you passed all the steps. CHARMM-ui is quite robust. So if the initial structure of the protein and the pdb correctly formated and complete, CHARMM-GUI should work. Stéphane

Re: [gmx-users] Fwd: Adding new atom types

Hi Tom, Thanks for the informative response. For the Gromos FF the gen-pairs is "no" and then the 1-4 interactions are taken from the parameters existed [ pairtypes ], if I change the gen-pairs to "yes" in Gromos FF, would you please confirm me that the parameters in [ pairtypes ] is still in

Re: [gmx-users] minimization is not converging (Bratin Kumar Das)

Dear ABEL, I tried CHARMM-gui but the charmm gui is getting failed for my system. On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane wrote: > Hi > > Did you try to use CHARMM-gui and use the gromacs files generated for this > system to see if your problem is resolved? > >

Re: [gmx-users] Workstation choice

Thank you, to use these tests isn’t a problem, but available workstation are too old, so test results won’t be helpful in choosing actual components. I have an access to high-performance cluster, but it also couldn’t be the basis because of its high cost. If it is hard to give the certain

[gmx-users] Functional Mode Analysis (FMA)

Hi Eduardo, The FMA tool is not yet included in the official distributed GROMACS version, but it is under code review. You can build GROMACS with the FMA tool from the attached tar ball of the development version that is currently being reviewed. The FMA tool can then be called as gmx fma

[gmx-users] Functional Mode Analysis (FMA)

Hello! I'd like to know if the current version of gromacs has the fma tool, as described in this paper: * https://doi.org/10.1371/journal.pcbi.1000480 It is said in this page: http://www3.mpibpc.mpg.de/groups/de_groot/fma.html , that the fma tool should be included from version 5.1

Re: [gmx-users] minimization is not converging (Bratin Kumar Das)

Hi Did you try to use CHARMM-gui and use the gromacs files generated for this system to see if your problem is resolved? Stéphane -- Message: 5 Date: Thu, 6 Sep 2018 19:55:07 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org

[gmx-users] Warning: correlations not long enough

Dear All, In my simulations ,I have a Peptide in aqueous solution with a cosolvent. For more number of hydrogen bonds like peptide water, water-water, there are no warnings But for Peptide cosolvent, there are 315 hydrogen bonds and it does the acf as 315/315... It shows warning: correlations

[gmx-users] Hydrogen bond correlations do not start from 1

Dear All, Upon using the g_hbond command with -ac option to calculate forward lifetime,I see that the C(t) does not start from one and keeps varying for different systems like it starts from 0.8 or 0.6 etc... I have tried the normalize flag but to no avail. Will the lifetime output be reliable?

Re: [gmx-users] Fwd: Adding new atom types

The GROMOS force fields are somewhat different to the others in that they provide specific 1-4 interactions by having several different C12 parameters for one atomtype (in some cases). The C12 value used depends upon the atomtypes involved in the interactions (see tables 7 and 8 of

[gmx-users] Fwd: Adding new atom types

Dear all, Any idea please about my both questions below? The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule about c12 in either sections! Thanks. Alex -- Forwarded message - From: Alex

Re: [gmx-users] minimization is not converging

Thank you sir On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul wrote: > > > On 9/6/18 10:09 AM, Bratin Kumar Das wrote: > > Respected Dr. Justin > > To avoid the complicacy I solvated > > only the protein pdb in a pbc box and tried for minimizatin. There also > >

Re: [gmx-users] minimization is not converging

On 9/6/18 10:09 AM, Bratin Kumar Das wrote: Respected Dr. Justin To avoid the complicacy I solvated only the protein pdb in a pbc box and tried for minimizatin. There also minimization is not converging. Sir, till now I learned to carry out protein ligand

Re: [gmx-users] minimization is not converging

Respected Dr. Justin To avoid the complicacy I solvated only the protein pdb in a pbc box and tried for minimizatin. There also minimization is not converging. Sir, till now I learned to carry out protein ligand system md simulation successfully. I tried all

Re: [gmx-users] minimization is not converging

On 9/6/18 9:51 AM, Bratin Kumar Das wrote: Respected Dr Justin, I took one membrane protein pdb file and converted it to .gro using pdb2gmx. Next I builded and packed the POPC phospholipids bylayer using vmd membrane builder plugin. Subsequently I

Re: [gmx-users] minimization is not converging

Respected Dr Justin, I took one membrane protein pdb file and converted it to .gro using pdb2gmx. Next I builded and packed the POPC phospholipids bylayer using vmd membrane builder plugin. Subsequently I solvated the system in vmd only. The entire system was

Re: [gmx-users] minimization is not converging

On 9/6/18 9:34 AM, Bratin Kumar Das wrote: Respected Dr Justin, In pdb2gmx command i used -ignh flag to ignore the hydrogens. Previously with out using this flag gave missing atom error. May be some hydrogens were missed. Is it possible that the error

Re: [gmx-users] minimization is not converging

Respected Dr Justin, In pdb2gmx command i used -ignh flag to ignore the hydrogens. Previously with out using this flag gave missing atom error. May be some hydrogens were missed. Is it possible that the error happening due to the flag (ignh). On Thu, Sep 6,

Re: [gmx-users] minimization is not converging

On 9/6/18 8:04 AM, Bratin Kumar Das wrote: Respected Dr. Justin, Thanking you for your valuable advice. Actually, I also tried to minimised the protein alone in the solvent without the membrane. so, result was similar. The system bowed up similarly. Is it

Re: [gmx-users] minimization is not converging

Respected Dr. Justin, Thanking you for your valuable advice. Actually, I also tried to minimised the protein alone in the solvent without the membrane. so, result was similar. The system bowed up similarly. Is it possible that due to inherent problem in topology

Re: [gmx-users] Justin paper 2010 pulling

On 9/6/18 2:29 AM, Rakesh Mishra wrote: While I have purely physics background. But, In my thinking, there are hydrogen bonds (electrostatic attractive interaction) between bp of both the strands of DNA/RNA which are perpendicular to helix direction. And the other thing you have chosen

Re: [gmx-users] minimization is not converging

On 9/6/18 7:47 AM, Bratin Kumar Das wrote: Dear all, I am running a membrane simulation with GCGR protein. I am getting the following warning and error Your system is unstable and blowing up. mdrun is telling you something is really bad around atom 15058, so start looking

[gmx-users] minimization is not converging

Dear all, I am running a membrane simulation with GCGR protein. I am getting the following warning and error gmx mdrun -v -s em_1.tpr -deffnm em_1 :-) GROMACS - gmx mdrun, 2016.5 (-: GROMACS is written by: Emile Apol Rossen

Re: [gmx-users] Orthorhombic structure and Lincs warnings

Your answers to questions 3 and 4 contradict each other in several ways. Do not use restraints or constraints (hint: LINCS is a constraint algorithm) and make sure your forcefield works. Right now it doesn't work, because a somewhat working forcefield does not lead to any crumpling, i.e. fix

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 173, Issue 12

Hi Alex , sorry to post my problem too many times. Coming back to your questions related to my problem 1. angles are 90,90,120 in x,y and z respectively. actually in quantum espresso this structure is little bit easy to handle. 2. without LINCS i haven't tried the simulation, i will do it

Re: [gmx-users] Justin paper 2010 pulling

While I have purely physics background. But, In my thinking, there are hydrogen bonds (electrostatic attractive interaction) between bp of both the strands of DNA/RNA which are perpendicular to helix direction. And the other thing you have chosen very fast velocity like (0.01, 0.001, 0.005 ).