Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Alex
What I meant is each of those files now has two columns, the first of which is of course time. What the second column is, especially for pullf, is a mystery to me. The total radial force? I wish someone who wrote the new pull code would clarify, because the result of wham now looks rather

[gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread Simon Kit Sang Chu
Hi everyone. I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It returned an error: Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. I can run mkdssp and it is placed in bin. Is it a compatibility problem here? Thanks in advance.

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread João Henriques
Also, if you're exporting DSSP="/.../dssp" and your bin contains mkdssp and not dssp, then that's going to fail for obvious reasons. Either export DSSP="/.../mkdssp" or create a link to mkdssp within the same directory with the name "dssp" (ln -s mkdssp dssp). Export and executable name must

[gmx-users] Error while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3)

2018-03-13 Thread 신동규
I am trying to install the latest GROMACS on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3) but got the following error when issuing cmake command. My command was: cmake .. -DGMX_GPU=on -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON I tried with option -DGMX_SIMD=AVX_512

Re: [gmx-users] computation/memory modifications

2018-03-13 Thread Mahmood Naderan
No idea? Any feedback is appreciated. Regards, Mahmood On Friday, March 9, 2018, 9:47:33 PM GMT+3:30, Mahmood Naderan wrote: Hi, I want to do some tests on the lysozyme tutorial. Assume that the tutorial with the default parameters which is run for 10ps, takes

[gmx-users] Error with CHARMM36 force field

2018-03-13 Thread laurenmr
Hi Gromacs Users, I have downloaded the latest version of the CHARMM36M force field. My aim is to compare a simulation using CHARMM36M and CHARMM36. In the forcefield.itp there is an 'if' statement allowing the user to switch to the old CHARMM36 force field by directing to the old cmap itp:

[gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Alex
Hi all, There seems to be a problem with the new pull code when it comes to using it for umbrella sampling with 'distance' directive for WHAM (the original thread is my earlier exchange with Justin in '[gmx-users] seeming paradox with gmx wham'). In order to subdue unknown statement errors,

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread João Henriques
"Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option." Did you follow the error message suggestion? With DSSP 2.2.1 you need to set "-ver 2" on your gmx do_dssp command. J On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu

Re: [gmx-users] Mentioning LJ Cutoff in mdp file

2018-03-13 Thread Mark Abraham
Hi, What does the .mdp documentation say for rvdw-switch and rvdw? Mark On Tue, Mar 13, 2018 at 11:11 AM Tushar Ranjan Moharana < tusharranjanmohar...@gmail.com> wrote: > Hi Everyone, > I want to use LJ interaction cutoff at 12 Å and treat LJ smoothly between > 10 and 12 Å. Does the following

Re: [gmx-users] Error with CHARMM36 force field

2018-03-13 Thread laurenmr
Hi Mark, Thanks for the reply. I use GROMACS-5.1.4 and I just use standard Linux editors. Please find my mdp file attached. When I check in the file "old_c36_cmap.itp" I do find very long lines (> 4095 characters). Could this mean that this force field file is not compatible with this

Re: [gmx-users] rvdw and rcoulomb

2018-03-13 Thread Ahmed Mashaly
Thanks guys It is AMBER ff Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 for continuation with no effect on the results? And if I do the other restarts starting from 1 or it will give different results? On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll

Re: [gmx-users] Error with CHARMM36 force field

2018-03-13 Thread laurenmr
Hi Mark, Thanks for the reply. I will contact the relevant person! Thanks, Lauren On 13/03/2018 17:40, Mark Abraham wrote: Hi, Yes, I guess it must be somehow incompatible. Maybe it worked with an older version of GROMACS that worked differently - the mdp handling has had some cleaning up

Re: [gmx-users] Error with CHARMM36 force field

2018-03-13 Thread laurenmr
Hi Justin, Thanks for the reply. Will download now. Thanks, Lauren On 13/03/2018 17:50, Justin Lemkul wrote: On 3/13/18 5:47 AM, laurenmr wrote: Hi Mark, Thanks for the reply. I will contact the relevant person! This was a bug very briefly when the latest tarball went online. I

Re: [gmx-users] Error while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3)

2018-03-13 Thread Mark Abraham
Hi, On Tue, Mar 13, 2018 at 7:31 AM 신동규 wrote: > I am trying to install the latest GROMACS on Dell EMC T640(Xeon Gold > 6152) with Tesla K880 GPU (RHEL 7.3) but got the following error when > issuing cmake command. > > My command was: > > cmake .. -DGMX_GPU=on

Re: [gmx-users] Error with CHARMM36 force field

2018-03-13 Thread Justin Lemkul
On 3/13/18 5:47 AM, laurenmr wrote: Hi Mark, Thanks for the reply. I will contact the relevant person! This was a bug very briefly when the latest tarball went online. I fixed it months ago. Please just download the latest tarball from

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread Simon Kit Sang Chu
Hi João, Thanks for your suggestion. Unfortunately, the error persists. I thought -ver 2 was the default value. Regards, Simon 2018-03-13 15:58 GMT+08:00 João Henriques : > "Fatal error: Failed to execute command: Try specifying your dssp version > with the -ver

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread Mark Abraham
Hi, gmx do_dssp -h says everything there is to say about how to get this to work. I've no idea what mkdssp is, but unless it does the same things as dssp, it won't work. Mark On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu wrote: > Hi João, > > Thanks for your

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread Simon Kit Sang Chu
Thank you, Joe. I re-ensure that dssp works in my case. I tried: dssp prod-protein.pdb -o test.dssp The result looks fine without error text. Simon 2018-03-13 17:24 GMT+08:00 Joe Jordan : > You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/ > It is also in

[gmx-users] Mentioning LJ Cutoff in mdp file

2018-03-13 Thread Tushar Ranjan Moharana
Hi Everyone, I want to use LJ interaction cutoff at 12 Å and treat LJ smoothly between 10 and 12 Å. Does the following in .mdp file reflect the same? rvdw-switch = 0.2 rvdw = 1 Kindly Reply. Thanks a lot. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student,

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Viveca Lindahl
Hi Alex, If you think this is a bug introduced in gromacs 2018, perhaps you could file a bug report on https://redmine.gromacs.org/? Attaching tpr's (or run setups) both for the 2018 and the 5.04 version together with an md.log would be helpful. -- Viveca On Tue, Mar 13, 2018 at 7:38 AM, Alex

Re: [gmx-users] computation/memory modifications

2018-03-13 Thread Justin Lemkul
On 3/13/18 2:49 AM, Mahmood Naderan wrote: No idea? Any feedback is appreciated. You likely missed my reply: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-March/119068.html -Justin Regards, Mahmood On Friday, March 9, 2018, 9:47:33 PM GMT+3:30, Mahmood Naderan

Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

2018-03-13 Thread Douwe Pollmann
Hi Mark, I use the Cb's to define a plane, and I use virtual sites to place beads in that plane. So the Cb's do not have non-bonded interactions with other beads, but they feel a force via the virtual sites. The problem is that my simulations are very unstable and that this is probably due to the

Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

2018-03-13 Thread Mark Abraham
Hi, If there's no interactions with CB then what's the point? Mark On Tue, Mar 13, 2018, 09:28 Douwe Pollmann wrote: > Hi Mark, > > Thanks for your reaction! > > 2018-03-12 18:08 GMT+01:00 Mark Abraham : > > > Hi, > > > > On Mon, Mar 12, 2018

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread Mateusz Bieniek
I had a similar issue with dssp which suddenly stopped working. Switching to x86 binary worked for me. Linux Arch Mat On Tue, 13 Mar 2018, 09:25 Joe Jordan, wrote: > You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/ > It is also in the ubuntu repo. > You

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread João Henriques
Ok, there's quite a lot going on here. The mkdssp the OP talks about is the default name for the executable you get upon compilation from source. Naming it dssp makes more sense, so that's why I suggested making a link called dssp. Either way, it shouldn't matter because if you give the right path

Re: [gmx-users] rvdw and rcoulomb

2018-03-13 Thread Justin Lemkul
On 3/13/18 5:17 AM, Ahmed Mashaly wrote: Thanks guys It is AMBER ff Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 for continuation with no effect on the results? And if I do the other restarts starting from 1 or it will give different results? You shouldn't

Re: [gmx-users] Error with CHARMM36 force field

2018-03-13 Thread Mark Abraham
Hi, Yes, I guess it must be somehow incompatible. Maybe it worked with an older version of GROMACS that worked differently - the mdp handling has had some cleaning up over time, and some buggy behaviours may have been inadvertently depended on. Perhaps this should be brought to the attention of

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Justin Lemkul
On 3/13/18 2:38 AM, Alex wrote: Hi all, There seems to be a problem with the new pull code when it comes to using it for umbrella sampling with 'distance' directive for WHAM (the original thread is my earlier exchange with Justin in '[gmx-users] seeming paradox with gmx wham'). In order to

Re: [gmx-users] Possible to use SETTLE for non-water molecules or switch off LINCS/SHAKE?

2018-03-13 Thread Douwe Pollmann
Hi Mark, Thanks for your reaction! 2018-03-12 18:08 GMT+01:00 Mark Abraham : > Hi, > > On Mon, Mar 12, 2018 at 4:19 PM Douwe Pollmann > wrote: > > > Dear Gromacs users, > > > > I am currently working on a coarse-grained model where I want to

Re: [gmx-users] Error with CHARMM36 force field

2018-03-13 Thread Mark Abraham
Hi, What version of GROMACS is this? Did you edit your file using an unsuitable editor, such as anything on Windows? Mark On Tue, Mar 13, 2018 at 9:20 AM laurenmr wrote: > Hi Gromacs Users, > > I have downloaded the latest version of the CHARMM36M force field. My >

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread João Henriques
Is the export consistent with the executable name? J On Tue, Mar 13, 2018 at 9:55 AM, Simon Kit Sang Chu wrote: > Hi João, > > Thanks for your suggestion. Unfortunately, the error persists. I thought > -ver 2 was the default value. > > Regards, > Simon > > 2018-03-13

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread Simon Kit Sang Chu
Hi everyone, I linked dssp as mkdssp and it still does not work. I try to run dssp in terminal. This is the result. mkdssp 2.2.1 options: -h [ --help ] Display help message -i [ --input ] argInput file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

2018-03-13 Thread Joe Jordan
You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/ It is also in the ubuntu repo. You should to get mkdssp and/or dssp to work on their own and if you can't then your problem is not with gmx. On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu wrote: > Hi

[gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Dilip H N
Hello, I want to calculate Hydrogen bonding between C-alpha of glycine and the oxygen atom of water molecules. So, i gave the command as:- gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg but i got the error as: Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms) Found

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Erik Marklund
Dear Dilip, The Calpha is not considered a hbond donor. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Justin Lemkul
On 3/13/18 7:16 AM, Justin Lemkul wrote: On 3/13/18 2:38 AM, Alex wrote: Hi all, There seems to be a problem with the new pull code when it comes to using it for umbrella sampling with 'distance' directive for WHAM (the original thread is my earlier exchange with Justin in '[gmx-users]

Re: [gmx-users] rvdw and rcoulomb

2018-03-13 Thread Ahmed Mashaly
Dear Justin, What do you mean by incorrect? I understand it is higher than it should be (0.8 - 1 nm), it will consume more time, but won't give wrong results, am I correct? Kind Regards, Ahmed From: Justin Lemkul To: gmx-us...@gromacs.org

Re: [gmx-users] rvdw and rcoulomb

2018-03-13 Thread Justin Lemkul
On 3/13/18 7:23 AM, Ahmed Mashaly wrote: Dear Justin, What do you mean by incorrect? I understand it is higher than it should be (0.8 - 1 nm), it will consume more time, but won't give wrong results, am I correct? With PME, the value of rcoulomb becomes somewhat irrelevant, but in

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Jeremy T First
Hi Dilip, There is quite a bit of literature, especially recently, that considers the alpha carbon as a hydrogen bond donor. How well this is represented in your simulation will depend on your force field. You will likely need to develop your own gromacs tool to calculate this, but it should be

Re: [gmx-users] computation/memory modifications

2018-03-13 Thread Justin Lemkul
On 3/13/18 9:50 AM, Mahmood Naderan wrote: Sorry about that. I didn't see that in the inbox. Excuse me... What am I thinking about are some notes in the tutorial. For example The above command centers the protein in the box (-c), and places it at least 1.0 nm from the box >edge (-d 1.0).

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Erik Marklund
The point is that Calpha don’t form hydrogen bonds. Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se On 13 Mar

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Justin Lemkul
On 3/13/18 10:17 AM, Alex wrote: Justin, You may have a situation that requires manual assignment of pull_group1_pbcatom1, as the automatic choice of Sorry, that should be pull_group1_pbcatom. Must remind myself not to email before coffee... Did you mean pull_group2_pbcatom? In my

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Dilip H N
Then how can i calculate the hydrogen bonding between C-alpha and Oxygen atom of water molecules..?? What are the other possible ways..?? Sent with Mailtrack On Tue, Mar 13, 2018 at

Re: [gmx-users] Error while Installing GROMACS 2018 on Dell EMC T640(Xeon Gold 6152) with Tesla K880 GPU (RHEL 7.3)

2018-03-13 Thread 신동규
Dear Mark, Thank you for your kind suggestion. I also read your other suggestion but I did not know what your solution meant at that time. I installed devtoolset-6 (7 is not working) in RHEL and commanded cmake successfully. Thank you again Dongkyu 2018-03-13 18:04 GMT+09:00 Mark Abraham

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Erik Marklund
A shortcut would be to only look at the C-O distance, which can be done with gmx hbond without modification. Kind regards, Erik > On 13 Mar 2018, at 15:01, Jeremy T First wrote: > > Hi Dilip, > > There is quite a bit of literature, especially recently, that considers

Re: [gmx-users] computation/memory modifications

2018-03-13 Thread Mahmood Naderan
Sorry about that. I didn't see that in the inbox. Excuse me... What am I thinking about are some notes in the tutorial. For example >The above command centers the protein in the box (-c), and places it at least >1.0 nm from the box >edge (-d 1.0). The box type is defined as a cube (-bt >cubic)

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Alex
Justin, You may have a situation that requires manual assignment of pull_group1_pbcatom1, as the automatic choice of Sorry, that should be pull_group1_pbcatom. Must remind myself not to email before coffee... Did you mean pull_group2_pbcatom? In my case: pull_group1_name    = K

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Alex
It appears that things have improved... I am just glancing and pullf and pullx data from the first sample config and both contain only one value, even though we set dim to 3D. Does this make sense? Thanks, Alex On 3/13/2018 8:18 AM, Justin Lemkul wrote: On 3/13/18 10:17 AM, Alex wrote:

Re: [gmx-users] Regarding minimum size

2018-03-13 Thread Chhavi Yadav
Hi, why is calling mdrunner twice a problem? I get the correct value when mdrunner runs the first time. Why do I get the error only during the second time considering I am not anyway doing any settings during both the times? Thanks, Chhavi On Mon, Mar 12, 2018 at 6:24 PM, Mark Abraham

Re: [gmx-users] Regarding minimum size

2018-03-13 Thread Mark Abraham
Hi, On Tue, Mar 13, 2018 at 4:11 PM Chhavi Yadav wrote: > Hi, > > why is calling mdrunner twice a problem? > Because nobody wrote the code with that in mind. There's a lot of things that are built around the assumption that mdrun will start, and then stop, and nothing happens

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

2018-03-13 Thread Debdas Dhabal
Dear Mark, It would be very grateful if you could please comment on my confusion mentioned above. Thank you very much. With regards Debdas On Mon, Mar 12, 2018 at 4:20 PM, Debdas Dhabal wrote: > Dear Mark, > > Thanks for your response. Yes, I have gone through that

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Justin Lemkul
On 3/13/18 10:32 AM, Alex wrote: It appears that things have improved... I am just glancing and pullf and pullx data from the first sample config and both contain only one value, even though we set dim to 3D. Does this make sense? I haven't used the 2018 pull code yet. Presumably this is

[gmx-users] Long Simulations in Batch GMX 2018

2018-03-13 Thread R
Dear all, I am doing a simulation of protein of my interest. I could run the simulation following the lysozyme tutorial. I am using 2018 version for gromacs. To start with, I ran the simulation for 1 ns. I want to run long simulation though want to make sure that each trajectory files has a

[gmx-users] long simulation in batch

2018-03-13 Thread roli . singh
Dear all, I am doing a simulation of protein of my interest. I could run the simulation following the lysozyme tutorial. I am using 2018 version for gromacs. To start with, I ran the simulation for 1 ns. I want to run long simulation though want to make sure that each trajectory files has a

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Alex
It's the force on the spring connecting the two groups. So, then, it's what I said. In any case, I must say that the probe along Z was more representative of the reality: a hemispherical slice probes a circle near the surface of the membrane, which has nothing to do with the pore, but

Re: [gmx-users] GMX 2018 and 'distance' pull

2018-03-13 Thread Justin Lemkul
On 3/13/18 4:19 PM, Alex wrote: What I meant is each of those files now has two columns, the first of which is of course time. What the second column is, especially for pullf, is a mystery to me. The total radial force? I wish someone who wrote the new pull It's the force on the spring

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

2018-03-13 Thread Shaun Tung
unsubscribe On Tue, Mar 13, 2018 at 1:53 PM, Mark Abraham wrote: > Hi, > > I already suggested where to go and find the answer, but you looked > somewhere else... The PDF you linked is kindly contributed by another user, > but not official. Anyway, apparently my memory

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

2018-03-13 Thread Mark Abraham
Hi, I already suggested where to go and find the answer, but you looked somewhere else... The PDF you linked is kindly contributed by another user, but not official. Anyway, apparently my memory is wrong and you can't do what you want. From the reference manual: If you want to have different

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 53

2018-03-13 Thread Jo
Hello, I have looked in the manual and tried the adjustments for verlet-buffer-tolerance and rlist (with no sucess), but I did not find a plot for this? Can you direct me to this? I've copied my mdp below if anyone could give me some insight. Thanks, Jo RUN PARAMETERS integrator

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 53

2018-03-13 Thread Mark Abraham
Hi, Please don't reply to digests. Please don't subscribe to digests if you actually want to post and discuss :-) See figure 3.5, or search for "drift" ;-) Mark On Tue, Mar 13, 2018 at 6:28 PM Jo wrote: > Hello, > > I have looked in the manual and tried the adjustments

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

2018-03-13 Thread Debdas Dhabal
Dear Mark, Many many thanks for your kind suggestion. I have also gone through the official Gromacs manual about table potential initially. But I was in a bit confusion. Thanks again Warm regards Debdas On Tue, Mar 13, 2018 at 1:53 PM, Mark Abraham wrote: > Hi, > >