Re: [gmx-users] Cavity in the system after NVT equilibration

The cavity, which is due to negative pressure in the system, might imply one of the two things: The Box is too big for the system or that the MD simulation implodes the system somehow. I have seen issues like these when the system is not well minimized and has some obvious artefacts like "broken"

Re: [gmx-users] Cavity in the system after NVT equilibration

Equilibration under NVT is a very bizarre approach, I am not even going to ask why you're doing this. I am known for perverse use of Gromacs, but please follow EM > NPT equilibration (Berendsen thermostat, etc) > production. The fact that you don't see the cavity at high temperature is that y

[gmx-users] Cavity in the system after NVT equilibration

Dear all, I have a system containing 4000 water molecules+700 of molecule A + 300 of molecule B. After minimization, the system undergoes a 2ns NVT equalization at 298.15 K which gives a big cavity in the system at the end, whereas the cavity does not show up at 650 K equlibration. But what I need

[gmx-users] Water in hydrophobic core of POPC lipid bilayer

Hello, I have successfully completed the KALP-15 in DPPC membrane tutorial recently and have since moved on to setting up my own protein-membrane system. For my system I am using POPC lipid parameters with GROMOS 53a6 ff obtained from the Lipidbook (2010 Poger and Mark version). After solvating

Re: [gmx-users] Looking for a Gromacs' tool to find lipid molecules which are located in a shell in the x-y plane around a drug molecule intercalated in a bilayer

Hi Seyed, You might want to take a look at the modified version of g_order (gmx order) provided as part of the SI of one of my papers: https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.7b00643 This code should be able to calculate order parameters at defined radial distances around a central o

Re: [gmx-users] Dangling bond error using Amber force field.

Hi Mark, Got it! Thank you so much! I replaced the Terminal of each chain with the corresponding NME residues and now it recognized the NME as the end terminal. Now, it seems work. I have been struggling for days. Thanks a lot for the help! Best Regards, Yang Wang Ph.D. student Departmen

Re: [gmx-users] Dangling bond error using Amber force field.

Hi, Thanks! Good to know. The PID is 2slk. And I use amber force field. Best Regards, Yang Wang Ph.D. student Department of Mechanical Engineering University of Texas at Dallas E-mail: yxw152...@utdallas.edu From: gromacs.

Re: [gmx-users] Dangling bond error using Amber force field.

Hi, The list can't accept attachments. It sounds like you need to set the chain IDs for your terminal residues to match the IDs of their chains. Mark On Fri, Jun 1, 2018, 17:19 Wang, Yang wrote: > Hi , > > I attached the PDB. It seems like cap ACE is listed in front of the main > body of the c

Re: [gmx-users] Dangling bond error using Amber force field.

Hi , I attached the PDB. It seems like cap ACE is listed in front of the main body of the chain but NME is separated from the chain and listed in the last part of the pbd file. And gromacs cannot tell that NME acrually belongs to each chain and thus separate all the NME to be a chain by itself.

Re: [gmx-users] Dangling bond error using Amber force field.

Hi, Chain 16 is clearly a problem (start and end residue is NME 8) but you'll have to look at the contents of the pdb file to understand its contents. Mark On Fri, Jun 1, 2018, 16:33 Wang, Yang wrote: > Hi, > > I am dealing with a protein model using Gromacs. I got the PDB file from > RCSB ban

[gmx-users] Dangling bond error using Amber force field.

Hi, I am dealing with a protein model using Gromacs. I got the PDB file from RCSB bank (PID: 2slk) and I modified the residue name according to the rtp file. Since the start terminal is ACE, I modified the end terminal from GLY/ALA to CGLY/CALA. I ran it with pdb2gmx command but I still got th

[gmx-users] covar warning

Hi, For PCA analysis i tried to run covar tool for my task, i got following warning ​ "​ WARNING: there are fewer frames in your trajectory than there are ​ ​ ​ degrees of freedom in your system. Only generating the first ​ ​ 400 out of 3564 eigenvectors and eigenvalues. ​"​ Why it generating 400

Re: [gmx-users] Thread-MPI error in GROMACS-2018

Hi, That error is a strong indicator of a code problem. There was a similar report on here a few days ago about a tMPI error. Please do open an issue at https://redmine.gromacs.org/ and attach those files above and your .tpr so we can reproduce the issue and try to find and fix its cause. Mark O

Re: [gmx-users] Partial charges

This has got nothing to do with Gromacs. A general comment: no, you should not neglect it. I am not sure what you mean by "QM," but the total charge of the system calculated by either DFT, or with Hartree-Fock, is _imposed_ and is not the result of calculations -- this sets up the sanity check