RE: [gmx-users] How to apply trjconv -nojump to a part of a system

Thanks mate, I am trying it now :) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Trayder Thomas Sent: Thursday, 11 July 2013 11:52 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to apply trjconv -nojump t

Re: [gmx-users] How to apply trjconv -nojump to a part of a system

VMD might do what you want with the PBC tools plugin (installed by default). http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/ unwrap being the equivalent of -nojump Otherwise, couldn't you just view your 2 trajectories simultaneously, one with protein the other not? -Trayder On Wed, Jul 10

Re: [gmx-users] 4.6.3 and MKL

I have the same feeling too but I'm not in charge of it unfortunately. Thank you, I appreciate. On 07/11/2013 07:15 AM, Mark Abraham wrote: No problems :-) (For the record, the fact that you had to brute-force static libraries in another thread does not fill me with confidence that your compiler

Re: [gmx-users] 4.6.3 and MKL

No problems :-) (For the record, the fact that you had to brute-force static libraries in another thread does not fill me with confidence that your compiler is installed correctly. But that is for you to judge! :-) On Thu, Jul 11, 2013 at 1:11 AM, Éric Germaneau wrote: > I see. > Thank you. > > >

Re: [gmx-users] 4.6.3 and MKL

I see. Thank you. On 07/11/2013 07:08 AM, Mark Abraham wrote: On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau wrote: Yes, as one can see in my first post. No, because we can't guess whether your icc is 11 or not. If so, you have a bunch of stuff that is not required. icc 11 has a magic flag f

Re: [gmx-users] 4.6.3 and MKL

I see. Thank you. On 07/11/2013 07:08 AM, Mark Abraham wrote: On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau wrote: Yes, as one can see in my first post. No, because we can't guess whether your icc is 11 or not. If so, you have a bunch of stuff that is not required. icc 11 has a magic flag f

Re: [gmx-users] 4.6.3 and MKL

On Thu, Jul 11, 2013 at 1:02 AM, Éric Germaneau wrote: > Yes, as one can see in my first post. No, because we can't guess whether your icc is 11 or not. If so, you have a bunch of stuff that is not required. icc 11 has a magic flag for using MKL, which GROMACS will use if given the chance. But I

Re: [gmx-users] 4.6.3 and MKL

Yes, as one can see in my first post. One thing is I don't know what libraries I need and in which order. Thanks, Eric. On 07/11/2013 06:58 AM, Mark Abraham wrote: Are you following the advice here? http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL On Thu

Re: [gmx-users] 4.6.3 and MKL

Are you following the advice here? http://www.gromacs.org/Documentation/Installation_Instructions#3.4.2._MKL On Thu, Jul 11, 2013 at 12:24 AM, Éric Germaneau wrote: > Dear all, > > Anyone have successfully built the 4.6.3 release using MKL? > I keep getting the following error message: > >--

Re: [gmx-users] implicit solvent

Yes, this is probably caused by a known bug in 4.6 that has been fixed for a month or two and mentioned in the release notes. Some work-arounds are suggested here http://redmine.gromacs.org/issues/1249, but you should probably update to 4.6.3 :-) Mark On Wed, Jul 10, 2013 at 5:43 PM, Cristina Dez

[gmx-users] 4.6.3 and MKL

Dear all, Anyone have successfully built the 4.6.3 release using MKL? I keep getting the following error message: -- Looking for DftiCreateDescriptor - not found CMake Error at CMakeLists.txt:1018 (message): Linking with MKL was requested, but was not successful. The include path

Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6

I figured out by using static libraries. On 07/10/2013 06:52 AM, Éric Germaneau wrote: Dear all, I call cmake the following way and get the error bellow: CC=mpicc CXX=mpicxx CMAKE_PREFIX_PATH=$FFTW3DIR:$CUDAPATH/include:$CUDAPATH/lib64:$CUDAPATH/bin \ /lustre/utility/bin/cmake \ -D

[gmx-users] Re: Fatal error: No donor atom 780

Never mind, everyone. Issue solved by always selecting the smaller index group first. On Wed, Jul 10, 2013 at 10:59 AM, yunshi11 . wrote: > Program g_hbond, VERSION 4.5.4 > Source code file: gmx_hbond.c, line: 823 > > Fatal error: > No donor atom 5226 > > > > On Wed, Jul 10, 2013 at 10:58 AM, yu

[gmx-users] Re: Fatal error: No donor atom 780

Program g_hbond, VERSION 4.5.4 Source code file: gmx_hbond.c, line: 823 Fatal error: No donor atom 5226 On Wed, Jul 10, 2013 at 10:58 AM, yunshi11 . wrote: > Hi all, > > I wonder what could be the cause of such a fatal error when using g_hbond > with -contact option. > > The two index group I

[gmx-users] Fatal error: No donor atom 780

Hi all, I wonder what could be the cause of such a fatal error when using g_hbond with -contact option. The two index group I chose have no overlap, but certain index group pairs worked while others did not and gave this fatal error. Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.or

Aw: [gmx-users] Figures of PCA analysis

There vectors.  Theres some good older papers explaining the whole thing from Van Gunstern, Berendsen, and some other good ones from de Groot that explain them well and includes combining them with other data analysis types, but I dont remeber the actual publications.  A few are in the mid 1990's,

[gmx-users] implicit solvent

Dear users, I am performing MD simulations of short peptides (from 7 to 45 units) in implicit solvent. I found quite bizarre results: all peptides unfold after few picosends, adopting a rather linear conformation until the end of MD, irrespective of temperature (I performed simulations at 200K, 40

Re: [gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

On 7/10/13 10:46 AM, Atila Petrosian wrote: Dear Baptiste Very thanks for your reply. Unfortunately, I have not access to InflateGro2. I encountered with error. If there are a script for InflateGro2 like InflateGro. please sent me perl script related to InflateGro2. It's freely available

[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

Dear Baptiste Very thanks for your reply. Unfortunately, I have not access to InflateGro2. I encountered with error. If there are a script for InflateGro2 like InflateGro. please sent me perl script related to InflateGro2. Best wishes. -- gmx-users mailing listgmx-users@gromacs.org http:/

Re: [gmx-users] Testing the performance of

Thanks! Mark. I got solution to my problem. For my system, setting pinoffset = 0, 16 and pinstride = 1 for two simultaneous simulations gave much satisfactory performance both for Verlet and Group cutoff-scheme. I tried it for 4 simultaneous simulations also with pinoffset = 0, 8, 16, 24 and pinst

Re: [gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

Hi, For a system with several component in the membrane, I think that InflateGRO 2 would be more appropriate. See http://code.google.com/p/inflategro2/ for the code and the related publication http://pubs.acs.org/doi/full/10.1021/ci3000453 Bests, Baptiste 2013/7/10 Atila Petrosian > Dear Jus

[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

Dear Justin Thanks for your quick reply. I want to study a system containing DOPC and cholesterol and drug. I correctly prepared gro files and topology parameters for this system. I did previous step (Step Two: Modify the Topology) without problem. I have 2 problems. 1) After I use trjconv -

[gmx-users] extreme projections

Dear users, I extracted separate extreme projections using g_anaeig. I have to make pictures which show the difference. Can you help me, someone who makes them using pymol before? -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

[gmx-users] Figures of PCA analysis

Dear users, I have a few questions about PCA analysis. I see the figures below in the most of the publications: 1.) Figure:Eigenvalues along the eigenvectors This figure gives contribution of eigenvalues along the eigenvectors to the overall motion of the protein??? 2.) Figure:the projection of th

Re: [gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

On 7/10/13 8:32 AM, Atila Petrosian wrote: Dear Justin I do your tutorial entitled " KALP15 in DPPC ". In Step Three: Defining the Unit Cell & Adding Solvent, You said "Use trjconv to remove periodicity ". When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact

[gmx-users] trjconv to remove periodicity (KALP15 in DPPC tutorial)

Dear Justin I do your tutorial entitled " KALP15 in DPPC ". In Step Three: Defining the Unit Cell & Adding Solvent, You said "Use trjconv to remove periodicity ". When I use trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact, gromacs tell me: Select group for output. Wh

RE: [gmx-users] Re: Re: Re: Re: Which/What is the adequate overlap

Hi, >-- Do I understand it right, that for instance (consider lambda step = 0.5) ONLY N(+Delta H(lambda=0) | lambda=0.5) AND N(-Delta H(lambda=0.5) | lambda=0) has to overlap, and then N(+Delta H(lambda=0.5) | lambda=1) AND N(-Delta H(lambda=1) | lambda=0.5) has to

[gmx-users] Re: Re: Re: Re: Which/What is the adequate overlap

Hi Thomas, thank you for your reply. Hi Mike, Your confusion might stem from a very simple issue. To see the overlap of the forward and backward distributions, you have to plot N(+Delta H(lambda=x) | lambda=y) and N(-Delta H(lambda=y) | lambda=x). Do I understand it right, that for instanc

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi there, You said ACPYPE didn't work… Can you give details? Have you try with GAFF first? If you don't mind, can you post me your molecule in private email? Thanks, Alan On 9 July 2013 22:34, Melchor S. wrote: > Sorry for the misunderstanding. I should had explained it better. > > I know th

Re: [gmx-users] Re: Multiple LINCS Warnings in NVT Equillibration

On 7/10/13 3:13 AM, ashish24294 wrote: I changed the cut-offs as follows, still isn't helping. I tried restraining the urea which also didn't work. I have attached the topology as well. topolurea.top The urea.itp looks suspicio

Re: Aw: [gmx-users] Umbrella sampling- force vs time plots

On 7/9/13 7:38 PM, rookie417 wrote: Thanks Justin and Stephan, One more question, while pulling from the interior of a multiple monomer micelle structure, I used higher force constants (5000 kJ/mol/nm^2) for position restraints on the reference group to keep the system intact. I am assuming t

Re: [gmx-users] How to apply trjconv -nojump to a part of a system

On 7/9/13 7:13 PM, Bin Liu wrote: Hi All, For the convenience of visualization, I need to remove the jump of one component (say a protein) of the system at the boundary. I don't need to, or say I need not to remove the jump of the other components (say a lipid bilayer), since otherwise the sys

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

On 7/9/13 5:34 PM, Melchor S. wrote: Sorry for the misunderstanding. I should had explained it better. I know that is a zwitterionic residue, I have run several simulations with the same PDB and with other forcefields. ACPYPE does not work, I tried it yesterday, but I have to check it. Antecha

[gmx-users] Re: Umbrella sampling- force vs time plots

Generally: Using a higher force constant and / or pulling velocity drives the system faster out of equilibrium, which results in higher rupture forces. Varying the force constant has two effects. The softer the potential is, the larger are the fluctuations in the coordinates but the lower are th

Re: [gmx-users] Xe atom

ya.. but there is experimental data to confirm the presence. can you help me to solve this problem On 9 July 2013 11:54, Dr. Vitaly Chaban wrote: > Is this, http://en.wikipedia.org/wiki/Xenon, your "Xe" ? If so, it will > obviously not sit in the binding site > > > Dr. Vitaly V. Chaban > >

Re: [gmx-users] FW: Inconsistent results between 3.3.3 and 4.6 with various set-up options

Just a note regarding the performance "issues" mentioned. You are using reaction-field electrostatics case in which by default there is very little force workload left for the CPU (only the bondeds) and therefore the CPU idles most of the time. To improve performance, use -nb gpu_cpu with multiple

Re: [gmx-users] Squishing or Stretching Membranes

Hey :) You can use editconf -scale to scale the system to the average box size. Cheers, Tsjerk On Jul 9, 2013 4:28 PM, "Mirco Wahab" wrote: On 09.07.2013 16:11, Neha wrote: > > I had a question about trjconv. After one of my simulations has... You could dump many structures from the last part

Re: [gmx-users] Frozen covalent bound atoms

constraints freeze_grps virtual_sites Cheers, Tsjerk On Jul 9, 2013 10:36 PM, "Nash, Anthony" wrote: Hi all, I would imagine this has been covered before, yet I don't think I have unearthed the right search inquiry yet. I want to make a dihedral angle along the length of a helical protein us

Re: [gmx-users] Problem with running REMD in Gromacs 4.6.3

Hi, Is affinity setting (pinning) on? What compiler are you using? There are some known issues with Intel OpenMP getting in the way of the internal affinity setting. To verify whether this is causing a problem, try turning of pinning (-pin off). Cheers, -- Szilárd On Tue, Jul 9, 2013 at 5:29 PM

[gmx-users] Re: Multiple LINCS Warnings in NVT Equillibration

I changed the cut-offs as follows, still isn't helping. I tried restraining the urea which also didn't work. I have attached the topology as well. topolurea.top *The nvt.mdp* title = UREA_in_WATER NVT equillibration ;define

[gmx-users] Re: Multiple LINCS Warnings in NVT Equillibration

Thank you!! But it still didn't work!! -- View this message in context: http://gromacs.5086.x6.nabble.com/Multiple-LINCS-Warnings-in-NVT-Equillibration-tp5009701p5009722.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.or