Re: [gmx-users] Temperature in CG production runs

On 10/30/18 7:26 AM, Yasser Almeida Hernández wrote: The reference temperature depends on what you want to model, and how well the force field reproduces the phase transition temperature of the lipids. If, for example, the force field requires higher temperature for a lipid type to remain

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

On 10/31/18 10:47 AM, Ramon Guixà wrote: Hi Justin, I do not have access to GPUs with ECC, but I have actually run the same tpr in different machines with different GPUs, including GTX 980, 1060 and 1080. In all cases, I get the same problem. Although they are all non-ECC cards, it is quite

Re: [gmx-users] Gmx distance

On 10/31/18 12:06 PM, rose rahmani wrote: Hi, I want to calculate distances between fixed tube in the middle of the box and amino acids(all are same type)around it. But gmx distance gives me the relative distance i mean AA can be front or back( can be 0.5 or -0.5 from tube) of tube but

Re: [gmx-users] Adding residue to .rtp file

Thank you for your valuable inputs. Yes i did checked ether parameters, diethylether have O-C (alkyl) bonding parameter as CC32A OC30A CC32A. but i dont find a parameter related to C(aromatic)-O bonding. similar one is tyrosine CA-OH1, but it may need validation on torsion terms?? can you please

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Ok, I mean, It makes sense what you say. I still I don't understand though how this has not been spotted before, I mean, I presume this combination is widely used (CHARMM+GROMACS+GPUs) and I have replicated the problem using versions 5, 2016, and 2018...? I know I sound a little desperate, but is

Re: [gmx-users] Strange pullx coordinates (PMF calculations)

On 10/31/18 11:43 AM, CROUZY Serge 119222 wrote: Dear gromacs users I've been running gromacs for several years, and enjoyed it.. I've been running PMF calculations for protein DNA interactions without problems until recently: Now I'm puzzled with the X coordinates being written in the

Re: [gmx-users] pcoupltype

On 10/30/18 3:42 PM, Kevin Boyd wrote: Hi, For membrane systems you typically want to use semi-isotropic pressure coupling. If instead you want to simulate *one* lipid (as a ligand) with a protein in solution, you should stick to isotropic pressure coupling. I've never heard of any

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

On 10/31/18 8:36 AM, Ramon Guixà wrote: Hi again, Just confirmed that when I run the same tpr file for 500 ns using only CPUs, no problems arise, please check it out here: https://drive.google.com/open?id=1aI2wr2GvNjCfj4c4J0pmgCzV0ak5FRE6

Re: [gmx-users] pcoupltype

Thank you very much Kevin and Justin for your information -Mensaje original- De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] En nombre de Justin Lemkul Enviado el: miércoles, 31 de octubre de 2018 13:53 Para:

[gmx-users] excutable dssp

Dear all I installed dssp on the gromacs version 5.1.4 and setenv as the following command: *export dssp=/usr/local/bin/gromacs/do_dssp* dssp was started to analyzed the protein structure, but after several minutes, we confront to this error: *failed to execute command, try specifying your dssp

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi Justin, I do not have access to GPUs with ECC, but I have actually run the same tpr in different machines with different GPUs, including GTX 980, 1060 and 1080. In all cases, I get the same problem. Although they are all non-ECC cards, it is quite unlikely that a bit flip is behind this,

[gmx-users] Gmx distance

Hi, I want to calculate distances between fixed tube in the middle of the box and amino acids(all are same type)around it. But gmx distance gives me the relative distance i mean AA can be front or back( can be 0.5 or -0.5 from tube) of tube but still |-0.5|=0.5 nm far from it. How can i have the

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

On 10/31/18 11:06 AM, Ramon Guixà wrote: Ok, I mean, It makes sense what you say. I still I don't understand though how this has not been spotted before, I mean, I presume this combination is widely used (CHARMM+GROMACS+GPUs) and I have replicated the problem using versions 5, 2016, and

Re: [gmx-users] excutable dssp

On 10/31/18 10:22 AM, marzieh dehghan wrote: Dear all I installed dssp on the gromacs version 5.1.4 and setenv as the following command: *export dssp=/usr/local/bin/gromacs/do_dssp* dssp was started to analyzed the protein structure, but after several minutes, we confront to this error:

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi again, Just confirmed that when I run the same tpr file for 500 ns using only CPUs, no problems arise, please check it out here: https://drive.google.com/open?id=1aI2wr2GvNjCfj4c4J0pmgCzV0ak5FRE6 I mean, is this a bug? Most

Re: [gmx-users] Adding residue to .rtp file

On 10/30/18 12:12 PM, Raji wrote: Hi Thank you for your input. 1. when attaching the alkyl chain with OH group in the aminoacid, to represent the bonded term C(aromatic)-O-C (alkyl). i took O as OC301 and C(alkyl) as CT2. But there is no bonded term for CA-OC301. How to import this by

Re: [gmx-users] Adding residue to .rtp file

On 10/31/18 10:56 AM, Raji wrote: Thank you for your valuable inputs. Yes i did checked ether parameters, diethylether have O-C (alkyl) bonding parameter as CC32A OC30A CC32A. but i dont find a parameter related to C(aromatic)-O bonding. similar one is tyrosine CA-OH1, but it may need

[gmx-users] Strange pullx coordinates (PMF calculations)

Dear gromacs users I've been running gromacs for several years, and enjoyed it.. I've been running PMF calculations for protein DNA interactions without problems until recently: Now I'm puzzled with the X coordinates being written in the pullx files (and thus taken as reaction coordinate values

Re: [gmx-users] pcoupltype

On 10/31/18 2:25 PM, ABEL Stephane wrote: Just my 2 cents If I recall well CHARMM36 and others force fields (such as lipid14) were initially parametrized and validated using the anisotropic pressure True, but only for a few tens of nanoseconds in the case of C36. The pressure coupling

[gmx-users] Zwitterionic amino acid topology parameters in CHARMM

Hi, I want to use zwitterionic form of AAs in CHARMM ff. I gave structure in Discovery studio and then use pdb2gmx to get its topology and ... files. But the number of atoms in topol.top and also some atom's partial charges are different from atoms and charges in aminoacids.rtp For example, in

Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

On 10/31/18 2:01 PM, rose rahmani wrote: Hi, I want to use zwitterionic form of AAs in CHARMM ff. I gave structure in Discovery studio and then use pdb2gmx to get its topology and ... files. But the number of atoms in topol.top and also some atom's partial charges are different from atoms

Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

Thank you, but I couldn't understand you exactly. My structures already have NH3+ and COO- . You mean everything is right? That's normal, yes? On Wed, 31 Oct 2018, 21:43 Justin Lemkul, wrote: > > > On 10/31/18 2:01 PM, rose rahmani wrote: > > Hi, > > > > I want to use zwitterionic form of AAs

Re: [gmx-users] 3. Re: Strange pullx coordinates (PMF calculations) (Justin Lemkul)

On 10/31/18 12:54 PM, CROUZY Serge 119222 wrote: Dear Justin Thanks for your fast answer OK for the larger group0 COM but as you say my reaction coordinate is the distance between the two COMs - The problem being that in the profile.xvg file the X coordinate reflects the box sizes and thus

[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

First, your init.pdb is really wacky. You've got a bleb in the membrane. That appears to heal rapidly during simulation, but the Z-axis fluctuations look pretty large to me. I suspect you're running into a known problem with P-R pressure coupling, which is that oscillations can get out of hand if

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

On 10/31/18 12:39 PM, Chris Neale wrote: First, your init.pdb is really wacky. You've got a bleb in the membrane. That appears to heal rapidly during simulation, but the Z-axis fluctuations look pretty large to me. I suspect you're running into a known problem with P-R pressure coupling,

[gmx-users] 3. Re: Strange pullx coordinates (PMF calculations) (Justin Lemkul)

Dear Justin Thanks for your fast answer OK for the larger group0 COM but as you say my reaction coordinate is the distance between the two COMs - The problem being that in the profile.xvg file the X coordinate reflects the box sizes and thus I can't superimpose the profiles coming from

[gmx-users] pcoupltype

Just my 2 cents If I recall well CHARMM36 and others force fields (such as lipid14) were initially parametrized and validated using the anisotropic pressure coupling scheme. So it make sense to use it instead of semi-isotropic pressure coupling. Moreover I found that if the membrane system is

Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

On 10/31/18 2:56 PM, rose rahmani wrote: Thank you, but I couldn't understand you exactly. My structures already have NH3+ and COO- . You mean everything is right? That's normal, yes? I was stating which terminal patches you should choose with pdb2gmx to transform the Phe .rtp topology

Re: [gmx-users] Crystal Surfaces in GROMACS

Hi, There are two main reasons there aren't any serious tutorials: first, Gromacs wasn't originally intended for this type of simulations and second, it's not clear what such a tutorial would describe. If you have a suitable interaction model for the material you'd like to simulate, the "usual"

Re: [gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

Hi Chris, I actually use the mdp file suggested by CHARMM-GUI. I figured they had tested this set-up extensively. Regarding the wacky init pdb, it has indeed been previously equilibrated using the Berendsen barostat for 20 ns, however, I will now run, as you suggest, a much longer equilibration

Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

i've tried it.But the results are exactly the same as i didn't apply patches. it doesn't make any difference. So what is the purpose of using -ter (COO- & NH3) when results are same in my case? On Wed, 31 Oct 2018, 22:49 Justin Lemkul, wrote: > > > On 10/31/18 2:56 PM, rose rahmani wrote: > >

[gmx-users] Crystal Surfaces in GROMACS

I've been trying to find out if there are any tutorials on simulating crystals (specifically crystal surfaces) using GROMACS; most of the tutorials I can find online seem to focus on finite-sized biomolecules and I don't know how the topology and run parameters would change with periodic

Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

On 10/31/18 4:23 PM, rose rahmani wrote: i've tried it.But the results are exactly the same as i didn't apply patches. it doesn't make any difference. So what is the purpose of using -ter (COO- & NH3) when results are same in my case? I don't follow. Topology generation requires the

Re: [gmx-users] Zwitterionic amino acid topology parameters in CHARMM

Oh, yes. I've got t now! Thank you so much Justin for your kind responses(as always;)). On Thu, Nov 1, 2018 at 12:23 AM Justin Lemkul wrote: > > > On 10/31/18 4:23 PM, rose rahmani wrote: > > i've tried it.But the results are exactly the same as i didn't apply > > patches. it doesn't make any

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 87

The forces and parameters aren't a problem, that's all been developed separately. My main concern is the connectivity of the crystal surface itself with periodic images. Is there a way to explicitly denote a connection between atoms in the box and their periodic images, or do I just have

Re: [gmx-users] Crystal Surfaces in GROMACS

On 10/31/18 6:55 PM, tca1 wrote: The forces and parameters aren't a problem, that's all been developed separately. My main concern is the connectivity of the crystal surface itself with periodic images. Is there a way to explicitly denote a connection between atoms in the box and their

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 87

Just to sort of summarize: there are only two things you need to do what I think you want to do: a topology generated by x2top from a set of coordinates in a properly sized box and the 'periodic-molecules' directive in the mdp file. This can allow all sorts of cute simulations, including what B.

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 87

The connectivity is set at the topology creation stage, which is separate from the mdp option "periodic-molecules." As long as the box size is commensurate with the crystal and the edges are properly periodic, gmx x2top used with proper options will create connectivity across the box without any

[gmx-users] Error: GROMACS GMX HLEIX segmentation Fault

Dear Gromacs Develeopment Team, Hello...I have the same segmentation fault of gmx helix even after updating with the revised version and/or applying the patch for the same. further I have alos tried to compile using the source-code of the latest version, I am facing the same segmentation