[gmx-users] Amber 14SB force-field problem with residue HID

Dear Users, I have encountered a problem with the Amber force-field downloaded from http://www.gromacs.org/Downloads/User_contributions/Force_fields. Whenever I feed this forcefield to pdb2gmx and get a residue HID for protein topology, it will cause error message: "No default Proper Dih. types".

Re: [gmx-users] Fwd: SIMD options

Hi Mark, thank you for your reply. I inspected CMakeError.log and CMakeOutputlog: though several errors were reported in the first one, no mention to GmxDetectCpu at all. When trying "cmake --debug-trycompile $builddir -UCPU_DETECTION_COMPILED", the output is: "debug trycompile on -- The

Re: [gmx-users] Residue 'UNK' not found in residue topology database

On 9/12/19 2:02 PM, Navneet Kumar Singh wrote: Yes, I succeed in running NVT and NPT without any error. But when I visualized the whole complex system (.gro) file in VMD/CHIMERA. It was like (Please download .JPG from the below link) https://fil.email/1pKxlHXy I have attached a snapshot. It

Re: [gmx-users] Residue 'UNK' not found in residue topology database

Yes, I succeed in running NVT and NPT without any error. But when I visualized the whole complex system (.gro) file in VMD/CHIMERA. It was like (Please download .JPG from the below link) https://fil.email/1pKxlHXy I have attached a snapshot. It looks like something weird problem with

Re: [gmx-users] Fwd: SIMD options

Hi, In that case, I would look at $builddir/CMakeFiles/CMakeError.log (and maybe $builddir/CMakeFiles/CMakeOutput.log) to see what was reported about that attempted compilation of GmxDetectCpu program. Depending what is learned, you might want to try your usual cmake call, and then cmake

Re: [gmx-users] Fwd: SIMD options

Hi Mark, actually running cmake in the output I can read "Did not detect build CPU vendor - detection program did not compile". Any suggestions about the origin of the issue and possible solutions? Thanks Stefano

Re: [gmx-users] Fwd: SIMD options

Hi, There will have been reports by cmake about whether the detection program compiled and/or ran successfully, which would be useful diagnostic information. Please run cmake in a fresh build directory and look for that. It is possible to run that program individually, if the issue is that it

Re: [gmx-users] Fwd: SIMD options

I cannot say about BIOS/firmware yet, I made a quite "standard" installation of centOS 7, but I'll try to check; as for cpu, for what it means, I made the stress test which brought up temperature for two hours together with gpu_burn, so I would exclude cooling failure. A further update: I

[gmx-users] Entropic effects in PMF at zero distance

The formula (5.283) from PDF manual or (3) in http://manual.gromacs.org/documentation/current/reference-manual/special/free-energy-implementation.html#potential-of-mean-force   V(r)=-(n-1)*kT*log(r) is obviously incorrect at r=0 for non singular potential (f.e. if "r" is the distance between

Re: [gmx-users] Fwd: SIMD options

On Thu, Sep 12, 2019 at 4:05 PM Stefano Guglielmo wrote: > > As an update, I have just tried a run with cpu only after compiling with > AVX2_128 and the workstation turned off after few minutes. That is suspicious. Perhaps a CPU cooling issue? Otherwise you may have a BIOS/firmware issue or,

Re: [gmx-users] Fwd: SIMD options

As an update, I have just tried a run with cpu only after compiling with AVX2_128 and the workstation turned off after few minutes. Mail priva di virus. www.avast.com

Re: [gmx-users] Fwd: SIMD options

On Thu, Sep 12, 2019 at 3:25 PM Stefano Guglielmo wrote: > > Hi Szilard, > thanks for your reply. > The compiler is gcc 4.8.5. That is ancient. From your cmake.out: -- Detection for best SIMD instructions failed, using SIMD - None -- SIMD instructions disabled Update your compiler toolchain

Re: [gmx-users] compressibility

On 9/11/19 6:50 AM, m g wrote: Dear Justin,I'm simulating 400 molecules of naphthalene in NPT ensemble at gas phase. Is it true that I set water compressibility in .mdp file? What must I do? Should I look for naphthalene isothermal compressibility in articles to use it?Thanks,Sana If

Re: [gmx-users] Residue 'UNK' not found in residue topology database

On 9/7/19 1:09 PM, Navneet Kumar Singh wrote: Thank You Sir! I just removed the ligand part from the system. Used Peptides+Water--Used pdb2gmx to create .gro file converted the ligand.pdb in to .gro using command *gmx editconf -f unk.pdb -o unk.gro* combined the peptides+water.gro and

Re: [gmx-users] Fwd: SIMD options

Hi Szilard, thanks for your reply. The compiler is gcc 4.8.5. I put below the link where you can find the files coming from cmake and the output for "AUTO" SIMD instruction. As for cpu only, as you had suggested previously I tried a run (after compiling with AVX2_256) and it worked without any

Re: [gmx-users] Fwd: SIMD options

On Thu, Sep 12, 2019 at 8:58 AM Stefano Guglielmo wrote: > > I apologize for the mistake, there was a typo in the object that could be > misleading, so I re-post with the correct object, > sorry. > > -- Forwarded message - > Da: Stefano Guglielmo > Date: mer 11 set 2019 alle ore

Re: [gmx-users] How can Build gromacs using MSVC on Win64 with AVX2?

On Thu, Sep 12, 2019 at 9:29 AM Tatsuro MATSUOKA wrote: > > >Those are kernels for legacy code that never use such simd anywhere > Doy you mean that gmxSimdFlags.cmake is not used for simd detection ? gmxSimdFlags.cmake detects the _flags_ necessary for a SIMD build. It is gmxDetectSimd.cmake /

Re: [gmx-users] How can Build gromacs using MSVC on Win64 with AVX2?

>Those are kernels for legacy code that never use such simd anywhere Doy you mean that gmxSimdFlags.cmake is not used for simd detection ? Tatsuro - Original Message - >From: Mark Abraham >To: Discussion list for GROMACS users ; Tatsuro >MATSUOKA >Date: 2019/9/12, Thu 14:39

[gmx-users] Fwd: SIMD options

I apologize for the mistake, there was a typo in the object that could be misleading, so I re-post with the correct object, sorry. -- Forwarded message - Da: Stefano Guglielmo Date: mer 11 set 2019 alle ore 17:17 Subject: SMD options To: Hi all, following my previous post